diff --git a/CHANGELOG.md b/CHANGELOG.md index d217034..d4ca805 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,7 @@ - argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/ - Use atomic writing for outputs +- Support GROOT v1.1.2 ### New Features diff --git a/README.md b/README.md index 980b2c3..c5b73bd 100644 --- a/README.md +++ b/README.md @@ -43,6 +43,7 @@ The `resistance_to_drug_classes` column will contain ARO numbers of the broader - [ABRicate](https://github.com/tseemann/abricate) (v1.0.1) with NCBI (v3.6), ResFinder (v4.1.11), MEGARes (v2.0), ARG-ANNOT (v5), ResFinderFG (v2) - [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder/src/master/) (v4.0) - [AMRFinderPlus](https://github.com/ncbi/amr) (v3.10.30) +- [GROOT](https://github.com/will-rowe/groot) (v1.1.2) ## Installation argNorm can be installed using pip: @@ -72,6 +73,7 @@ The only positional argument required is `tool` which can be: - `abricate` - `resfinder` - `amrfinderplus` +- `groot` The available options are: - `-h` or `--help`: shows available options and exits. @@ -82,6 +84,7 @@ The available options are: - DeepARG (`deeparg`) - MEGARes (`megares`) - ARG-ANNOT (`argannot`) + - `groot-core-db`, `groot-db`, `groot-resfinder`, `groot-argannot`, `groot-card` - `--hamronized`: use this if the input is hamronized by [hAMRonization](https://github.com/pha4ge/hAMRonization) - `-i` or `--input`: path to the annotation result - `-o` or `--output`: the file to save normalization results @@ -90,17 +93,20 @@ Use `argnorm -h` or `argnorm --help` to see available options. ```bash >argnorm -h -usage: argnorm [-h] [--db {sarg,ncbi,resfinder,deeparg,megares,argannot}] [--hamronized] [-i INPUT] [-o OUTPUT] {argsoap,abricate,deeparg,resfinder,amrfinderplus} +usage: argnorm [-h] + [--db {sarg,ncbi,resfinder,deeparg,megares,argannot,resfinderfg,groot-argannot,groot-resfinder,groot-db,groot-core-db,groot-card}] + [--hamronized] [-i INPUT] [-o OUTPUT] + {argsoap,abricate,deeparg,resfinder,amrfinderplus,groot} argNorm normalizes ARG annotation results from different tools and databases to the same ontology, namely ARO (Antibiotic Resistance Ontology). positional arguments: - {argsoap,abricate,deeparg,resfinder,amrfinderplus} + {argsoap,abricate,deeparg,resfinder,amrfinderplus,groot} The tool you used to do ARG annotation. -options: +optional arguments: -h, --help show this help message and exit - --db {sarg,ncbi,resfinder,deeparg,megares,argannot} + --db {sarg,ncbi,resfinder,deeparg,megares,argannot,resfinderfg,groot-argannot,groot-resfinder,groot-db,groot-core-db,groot-card} The database you used to do ARG annotation. --hamronized Use this if the input is hamronized (processed using the hAMRonization tool) -i INPUT, --input INPUT diff --git a/argnorm/cli.py b/argnorm/cli.py index 3e29f6f..9ee9173 100644 --- a/argnorm/cli.py +++ b/argnorm/cli.py @@ -11,10 +11,22 @@ def main(): 'namely ARO (Antibiotic Resistance Ontology).'), formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('tool', type=str.lower, - choices=['argsoap', 'abricate', 'deeparg', 'resfinder', 'amrfinderplus'], + choices=['argsoap', 'abricate', 'deeparg', 'resfinder', 'amrfinderplus', 'groot'], help='The tool you used to do ARG annotation.') parser.add_argument('--db', type=str.lower, - choices=['sarg', 'ncbi', 'resfinder', 'deeparg', 'megares', 'argannot', 'resfinderfg'], + choices=['sarg', + 'ncbi', + 'resfinder', + 'deeparg', + 'megares', + 'argannot', + 'resfinderfg', + 'groot-argannot', + 'groot-resfinder', + 'groot-db', + 'groot-core-db', + 'groot-card' + ], help='The database you used to do ARG annotation.') parser.add_argument('--hamronized', action='store_true', help='Use this if the input is hamronized (processed using the hAMRonization tool)') diff --git a/argnorm/data/groot_ARO_mapping.tsv b/argnorm/data/groot_ARO_mapping.tsv new file mode 100644 index 0000000..db09096 --- /dev/null +++ b/argnorm/data/groot_ARO_mapping.tsv @@ -0,0 +1,8951 @@ +Original ID ARO +(AGly)APH-Stph:HE579073:1778413-1779213:801 3002663 +(AGly)Aac(2')-Id:U72743:386-1018:533 3002526 +(AGly)Aac(3)-IIIb:L06160:984-1721:861 3002537 +(AGly)Aac(3)-IIIc:L06161:106-945:861 3002538 +(AGly)Aac(6')-Iae:AB104852:1935-2486:552 3002573 +(AGly)Aac-IIIa:X55652:1124-1939:816 3002536 +(AGly)Aac-IVa:X01385:244-1029:786 3002539 +(AGly)Aac2-Ia:L06156:264-800:537 3002523 +(AGly)Aac2-Ib:U41471:266-822:588 3002524 +(AGly)Aac2-Ic:U72714:373-918:546 3002525 +(AGly)Aac2-Ie:NC_011896:3039059-3039607:549 3002527 +(AGly)Aac3-I:AJ877225:5293-5757:465 3002528 +(AGly)Aac3-I:X15852:1250-1783:534 3002528 +(AGly)Aac3-IIa:X51534:91-951:861 3004621 +(AGly)Aac3-IIc:X54723:819-1679:861 3002535 +(AGly)Aac3-IId:EU022314:1-861:861 3004623 +(AGly)Aac3-IIe:EU022315:1-861:861 3004621 +(AGly)Aac3-IXa:M55427:274-1119:846 3002543 +(AGly)Aac3-Ib-Aac6-Ib:AF355189:1435-2439:1005 3002600 +(AGly)Aac3-Ib:L06157:555-1085:531 3002530 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3002892 +otr(B)_1_AF079900 3002892 +otr(C) 3002894 +otr(C)_1_AY509111 3002894 +patA 3000024 +patB 3000025 +penA_1_AF515059 3003937 +pexA 3004666 +pexA_1_HM537013 3004666 +pgpB 3003920 +pmrA 3000822 +poxtA 3004470 +pp-flo 3002812 +pp_cat 3002689 +qacA 3003046 +qacB 3003047 +qacE 3005009 +qacEdelta1 3005010 +qacG 3007015 +qacH 3003836 +qacJ 3007014 +qacL 3005098 +qepA1_1_AB263754 3004103 +qepA2_1_EU847537 3004103 +qepA3_1_JQ064560 3000448 +qepA4_1_KX580704 3004379 +qepA_1_FJ167861 3004379 +qnrA1_1_AY070235 3002707 +qnrA2_1_AY675584 3002708 +qnrA3_1_DQ058661 3002709 +qnrA4_1_DQ058662 3002710 +qnrA5_1_DQ058663 3002711 +qnrA6_1_DQ151889 3002712 +qnrA7_1_GQ463707 3002713 +qnrA8_1_KY554783 3002709 +qnrB10_1_DQ631414 3002724 +qnrB10_2_HM439644 3002724 +qnrB11_1_EF653270 3002725 +qnrB12_2_AM774474 3002726 +qnrB13_1_EU273755 3002727 +qnrB14_1_EU273757 3002728 +qnrB15_1_EU302865 3002730 +qnrB16_1_EU136183 3002731 +qnrB17_1_JN173051 3002732 +qnrB17_2_AM919398 3002732 +qnrB18_1_AM919399 3002733 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+sul1_31_AM040449 3000410 +sul1_32_EF592571 3000410 +sul1_33_AJ564903 3000410 +sul1_34_AY047357 3000410 +sul1_35_AB281183 3000410 +sul1_3_EU855787 3000410 +sul1_5_EU780013 3000410 +sul1_7_FJ715937 3000410 +sul1_8_JN581942 3000410 +sul1_9_AY963803 3000410 +sul2 3000412 +sul2_10_AM183225 3000412 +sul2_11_AY232670 3000412 +sul2_12_AF497970 3000412 +sul2_13_AJ289135 3000412 +sul2_14_AJ514834 3000412 +sul2_15_FJ968160 3000412 +sul2_17_U57647 3000412 +sul2_18_AJ830714 3000412 +sul2_19_AJ319822 3000412 +sul2_1_AF542061 3000412 +sul2_20_AJ830710 3000412 +sul2_2_GQ421466 3000412 +sul2_3_HQ840942 3000412 +sul2_5_AY524415 3000412 +sul2_6_FN995456 3000412 +sul2_7_HM486907 3000412 +sul2_8_AJ877041 3000412 +sul2_9_FJ197818 3000412 +sul3 3000413 +sul3_2_AJ459418 3000413 +sul4 3004361 +tap 3000343 +tcr3 3002893 +tcr3_1_D38215 3002893 +tet(0/32/0)_2_AJ295238 3007119 +tet(0/32/0)_3_NZ_AUJS01000017 3000190 +tet(0/32/0)_4_AINH01000038 3000190 +tet(0/32/0)_5_NZ_AINJ01000054 3000190 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3000192 +tet(S/M)_1_HM367711 3000186 +tet(S/M)_2_AY534326 3000192 +tet(T) 3000193 +tet(T)_1_L42544 3000193 +tet(T)_2_AY660530 3000193 +tet(V) 3000181 +tet(V)_1_AF030344 3000181 +tet(W) 3000194 +tet(W)_1_DQ060146 3000194 +tet(W)_2_AY049983 3007124 +tet(W)_3_AJ427421 3000194 +tet(W)_4_FN396364 3000194 +tet(W)_5_AJ427422 3000194 +tet(W/32/O) 3007124 +tet(W/32/O)_1_AM710601 3007122 +tet(W/32/O)_2_AM710602 3007122 +tet(W/32/O)_3_AM710603 3007122 +tet(W/32/O)_4_AM710604 3007122 +tet(W/32/O)_5_AM710605 3007122 +tet(W/N/W) 3004442 +tet(X) 3000205 +tet(X)_1_GU014535 3000205 +tet(X)_2_M37699 3000205 +tet(X)_3_AB097942 3005056 +tet(X1) 3005166 +tet(X3) 3004719 +tet(X4) 3004720 +tet(X5) 3005057 +tet(X6) 3005056 +tet(Y) 3000182 +tet(Y)_1_EF495198 3000182 +tet(Y)_2_AB089606 3000182 +tet(Z) 3000183 +tet(Z)_1_AF121000 3000183 +tetA(46) 3004032 +tetA(46)_1_HQ652506 3004032 +tetA(58) 3003980 +tetA(60) 3004035 +tetA(60)_1_KX000272 3004035 +tetA(P) 3000180 +tetA(P)_1_AB054980 3000180 +tetA(P)_2_L20800 3000180 +tetA(P)_3_AB001076 3000180 +tetB(46) 3004033 +tetB(46)_1_HQ652506 3004033 +tetB(58) 3003981 +tetB(60) 3004036 +tetB(60)_1_KX000273 3004036 +tetB(P) 3000195 +tetB(P)_1_NC_010937 3000195 +tet_1_M74049 3007127 +tlr(C)_1_M57437 3002827 +tlrC 3002827 +tmrB 3003059 +tsnR 3003060 +tva(A) 3004730 +ugd 3003577 +vanA 3000010 +vanB 3000013 +vanC 3000368 +vanD 3000005 +vanE 3002907 +vanF 3002908 +vanG 3002909 +vanH_in_vanA_cl 3002942 +vanH_in_vanB_cl 3002943 +vanH_in_vanD_cl 3002944 +vanH_in_vanF_cl 3002945 +vanH_in_vanM_cl 3002947 +vanH_in_vanO_cl 3002948 +vanH_in_vanP_cl 3007188 +vanI 3003723 +vanJ 3002914 +vanK_in_vanI_cl 3003727 +vanL 3002910 +vanM 3002911 +vanN 3002912 +vanO 3002913 +vanP 3007189 +vanR_in_vanA_cl 3002919 +vanR_in_vanB_cl 3002921 +vanR_in_vanC_cl 3002922 +vanR_in_vanD_cl 3002923 +vanR_in_vanE_cl 3002924 +vanR_in_vanF_cl 3002925 +vanR_in_vanG_cl 3002926 +vanR_in_vanI_cl 3003728 +vanR_in_vanL_cl 3002927 +vanR_in_vanM_cl 3002928 +vanR_in_vanN_cl 3002929 +vanR_in_vanO_cl 3002930 +vanR_in_vanP_cl 3007191 +vanS_in_vanA_cl 3002931 +vanS_in_vanB_cl 3002932 +vanS_in_vanC_cl 3002933 +vanS_in_vanD_cl 3002934 +vanS_in_vanE_cl 3002935 +vanS_in_vanF_cl 3002936 +vanS_in_vanG_cl 3002937 +vanS_in_vanL_cl 3002938 +vanS_in_vanM_cl 3002939 +vanS_in_vanN_cl 3002940 +vanS_in_vanO_cl 3002941 +vanS_in_vanP_cl 3007192 +vanT_in_vanC_cl 3002970 +vanT_in_vanE_cl 3002971 +vanT_in_vanG_cl 3002972 +vanT_in_vanN_cl 3002975 +vanTm_in_vanL 3002973 +vanTr_in_vanL 3002974 +vanU_in_vanG_cl 3004253 +vanV_in_vanB_cl 3004254 +vanW_in_vanB_cl 3002964 +vanW_in_vanG_cl 3002965 +vanW_in_vanI_cl 3003724 +vanXY_in_vanC 3002966 +vanXY_in_vanE 3002967 +vanXY_in_vanG 3003069 +vanXY_in_vanL 3002968 +vanXY_in_vanN 3002969 +vanX_in_vanA_cl 3002949 +vanX_in_vanB_cl 3002950 +vanX_in_vanD_cl 3003070 +vanX_in_vanF_cl 3002952 +vanX_in_vanI_cl 3003725 +vanX_in_vanM_cl 3002953 +vanX_in_vanO_cl 3002954 +vanX_in_vanP_cl 3007190 +vanY_in_vanA_cl 3002955 +vanY_in_vanB_cl 3002956 +vanY_in_vanD_cl 3002957 +vanY_in_vanF_cl 3002958 +vanY_in_vanG_cl 3002959 +vanY_in_vanM_cl 3002961 +vanZ_in_vanA_cl 3002962 +vanZ_in_vanF_cl 3002963 +vat(A)_1_L07778 3002840 +vat(B)_1_U19459 3002841 +vat(C)_1_AF015628 3002842 +vat(D)_1_L12033 3002843 +vat(E)_10_AY043212 3002844 +vat(E)_11_AY043213 3002844 +vat(E)_3_AF153312 3002844 +vat(E)_5_AJ488494 3002844 +vat(E)_7_AY043211 3002844 +vat(E)_8_AY043209 3002844 +vat(E)_9_AY043210 3002844 +vat(F)_1_AF170730 3003744 +vatA 3002840 +vatB 3002841 +vatC 3002842 +vatD 3002843 +vatE 3002844 +vatF 3003744 +vatH 3002845 +vga(A)LC_1_GQ891882 3002829 +vga(A)_1_M90056 3002829 +vga(A)_2_FN546261 3002829 +vga(B)_1_U82085 3000118 +vga(C)_1_GQ205627 3002832 +vga(C)_2_NC_013034 3002831 +vga(E)_1_FR772051 3002833 +vgaA 3002829 +vgaALC 3002830 +vgaB 3000118 +vgaC 3002831 +vgaD 3002832 +vgaE 3002833 +vgb(A)_1_M20129 3001307 +vgb(B)_1_AF015628 3001308 +vgbA 3001307 +vgbB 3001308 +vgbC 3003990 +vmlR 3004476 +vph 3003061 +ykkC 3003063 +ykkD 3003064 diff --git a/argnorm/data/manual_curation/groot_curation.tsv b/argnorm/data/manual_curation/groot_curation.tsv new file mode 100644 index 0000000..52990a0 --- /dev/null +++ b/argnorm/data/manual_curation/groot_curation.tsv @@ -0,0 +1,3 @@ +Original ID ARO Description +blaOXA-14_1_L38523 3001409 The starting of the CDS ('ATGAAAACATTTGCCGCATATGTAAT') was missing, so RGI couldn't find the corresponding ARG +blaTEM-199_1_JX050178 3001058 RGI couldn't detect the ARG as there was a 'T' added to the beginning of the nucleotide sequence which did not translate to the correct amino acid sequence. diff --git a/argnorm/lib.py b/argnorm/lib.py index a174ad6..5fa0812 100644 --- a/argnorm/lib.py +++ b/argnorm/lib.py @@ -12,7 +12,24 @@ MAPPING_TABLE_ARO_COL = 'ARO' TARGET_ARO_COL = 'ARO' -DATABASES = ['argannot', 'deeparg', 'megares', 'ncbi', 'resfinder', 'resfinderfg', 'sarg'] +DATABASES = [ + 'argannot', + 'deeparg', + 'megares', + 'ncbi', + 'resfinder', + 'resfinderfg', + 'sarg', + 'groot', +] + +groot_ref_databases = [ + 'groot-db', + 'groot-core-db', + 'groot-argannot', + 'groot-resfinder', + 'groot-card', +] _ROOT = os.path.abspath(os.path.dirname(__file__)) _ARO = None @@ -41,6 +58,9 @@ def get_aro_mapping_table(database): Returns: aro_mapping_table (DataFrame): A pandas dataframe with ARGs mapped to AROs. """ + + if 'groot' in database: + database = 'groot' aro_mapping_table = pd.read_csv( os.path.join(_ROOT, 'data', f'{database}_ARO_mapping.tsv'), @@ -51,20 +71,22 @@ def get_aro_mapping_table(database): manual_curation = pd.read_csv( os.path.join(_ROOT, 'data/manual_curation', f'{database}_curation.tsv'), sep='\t', index_col=0, dtype={'ARO': str}) - manual_curation['Database'] = aro_mapping_table['Database'].iloc[0] + if database != 'groot': + manual_curation['Database'] = aro_mapping_table['Database'].iloc[0] aro_mapping_table.drop(index=set(manual_curation.index) & set(aro_mapping_table.index), inplace=True) aro_mapping_table = pd.concat([aro_mapping_table, manual_curation]) aro_mapping_table['ARO'] = aro_mapping_table['ARO'].map(lambda a: f'ARO:{a}', na_action='ignore') return aro_mapping_table -def map_to_aro(gene, database): +def map_to_aro(gene, database, groot_ref_db=None): """ Description: Gets ARO mapping for a specific gene in a database. Parameters: gene (str): The original ID of the gene as mentioned in source database. - database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg and sarg + database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg, sarg, and groot + groot_ref_db (str, optional): name of reference db used by groot. Can be groot-argannot, groot-resfinder, groot-card, groot-core-db, or groot-db Returns: ARO[result] (pronto.term.Term): A pronto term with the ARO number of input gene. ARO number can be accessed using 'id' attribute and gene name can be accessed using 'name' attribute. @@ -72,10 +94,25 @@ def map_to_aro(gene, database): If ARO mapping is doesn't exist, None is returned. """ - if database not in ['ncbi', 'deeparg', 'resfinder', 'sarg', 'megares', 'argannot']: + if database not in DATABASES: raise Exception(f'{database} is not a supported database.') + if 'groot' in database and not groot_ref_db in groot_ref_databases: + raise Exception(f'{groot_ref_db} is not a valid groot reference database') mapping_table = get_aro_mapping_table(database) + + # Preprocess input gene & mapping table original ids if groot is being used + if 'groot' in database: + if groot_ref_db == 'groot-argannot': + gene = gene.split('~~~')[-1] + mapping_table.index = mapping_table.index.map(lambda x: ':'.join(str(x).split(':')[1:3])) + if groot_ref_db == 'groot-card': + gene = gene.split('.')[0] + if groot_ref_db in ['groot-db', 'groot-core-db']: + if 'card' in gene.lower(): + gene = gene.split('|')[-1] + else: + gene = gene.split('__')[1] try: result = mapping_table.loc[gene, 'ARO'] diff --git a/argnorm/normalize.py b/argnorm/normalize.py index 5a45534..528e381 100644 --- a/argnorm/normalize.py +++ b/argnorm/normalize.py @@ -1,5 +1,5 @@ from .normalizers import ARGSOAPNormalizer, \ - DeepARGNormalizer, AbricateNormalizer, ResFinderNormalizer, AMRFinderPlusNormalizer + DeepARGNormalizer, AbricateNormalizer, ResFinderNormalizer, AMRFinderPlusNormalizer, GrootNormalizer def normalize(ifile, tool : str, database : str, is_hamronized : bool): '''Normalize ARG tables @@ -20,6 +20,7 @@ def normalize(ifile, tool : str, database : str, is_hamronized : bool): 'argsoap': ARGSOAPNormalizer, 'deeparg': DeepARGNormalizer, 'resfinder': ResFinderNormalizer, + 'groot': GrootNormalizer }.get(tool) if normalizer is None: diff --git a/argnorm/normalizers.py b/argnorm/normalizers.py index b1bb7c7..fa07f80 100644 --- a/argnorm/normalizers.py +++ b/argnorm/normalizers.py @@ -1,4 +1,3 @@ -import os import pandas as pd try: pd.options.mode.copy_on_write = True @@ -158,3 +157,40 @@ def preprocess_ref_genes(self, ref_genes): ) return ref_genes.map(process_funcs_by_db[self.database]) +class GrootNormalizer(BaseNormalizer): + def __init__(self, database=None, is_hamronized=False) -> None: + if database not in ['groot-argannot', 'groot-resfinder', 'groot-db', 'groot-core-db', 'groot-card']: + raise Exception(f'{database} is not a supported database for groot.') + + super().__init__(database, is_hamronized) + + def load_input(self, input_file): + if self.is_hamronized: + return pd.read_csv(input_file, sep='\t') + return pd.read_csv(input_file, sep='\t', header=None) + + def preprocess_groot_db_inputs(self, gene_name): + processed_gene_name = str(gene_name).split('__')[1] + if 'card' in str(gene_name).split('__')[0].lower(): + processed_gene_name = processed_gene_name.split('|')[-1] + return processed_gene_name + + def get_input_ids(self, itable): + if self.is_hamronized: + col = 'gene_name' + else: + col = 0 + + if self.database == 'groot-argannot': + return itable[col].map(lambda x: x.split('~~~')[-1]) + if self.database == 'groot-card': + return itable[col].map(lambda x: x.split('.')[0]) + if self.database in ['groot-db', 'groot-core-db']: + return itable[col].map(self.preprocess_groot_db_inputs) + + return itable[col] + + def preprocess_ref_genes(self, ref_genes): + if self.database == 'groot-argannot': + return ref_genes.map(lambda x: ':'.join(str(x).split(':')[1:3])) + return ref_genes \ No newline at end of file diff --git a/db_harmonisation/README.md b/db_harmonisation/README.md index 144340d..41014ef 100644 --- a/db_harmonisation/README.md +++ b/db_harmonisation/README.md @@ -76,6 +76,105 @@ The RGI outputs of CDSs & contigs are combined with resfinder & argannot mapping > Note: as BacMet is now ignored, there will be less megares mappings (compared to when all of megares was run through RGI using `contig` mode) as loose hits from RGI won't be associated with BacMet entries. +# Groot Databases + +Groot uses `resfinder`, `CARD`, and `argannot`. +While the [groot documentation](https://groot-documentation.readthedocs.io/en/latest/groot-databases.html) says that the latest versions of card, argannot, and resfinder are used to create the groot db, only the latest version of the CARD database is downloaded, and older versions of resfinder and argannot (v3) are used - these were the latest versions of resfinder and argannot when the groot documentation was written. + +- `argannot` db that groot uses: https://www.mediterranee-infection.com/wp-content/uploads/2019/03/argannot-aa-v3-march2017.txt +- `resfinder` db that groot uses: https://bitbucket.org/genomicepidemiology/resfinder_db/src/dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2/ + +
+Here is the bash script that groot uses to create its database. You can view the code online here + +``` +#!/bin/env bash +# +# This script generates the groot-core-db and the groot-db +# +# It downloads the latest versions of the following databases: +# +# - argannot +# - resfinder +# - card +# - megares +# +# It then either: +# 1. groot-db: merge the databases, remove duplicates and then cluster +# or +# 2. groot-core-db: extract common ARGs from all databases and then cluster these common ARGs +# +# REQUIRES: Vsearch, SeqKit +# + +echo "making the groot and groot-core databases..." +mkdir tmp && cd $_ + +# Download the latest CARD database +mkdir card && cd $_ +wget --no-check-certificate -qO- https://card.mcmaster.ca/download | grep -Eo "download/0/broadstreet[a-zA-Z0-9./?=_-]*" | sort | uniq | tail -n 1 > card-db-version +cardLink=$(sed 's/^/https:\/\/card.mcmaster.ca\//g' card-db-version) +wget --no-check-certificate -O card-db.tar.gz $cardLink +tar -xvf card-db.* +awk '/>/{sub(">",">groot-db_CARD__")}1' nucleotide_fasta_protein_homolog_model.fasta > ../card-refs.fna +cd .. && rm -r card + +# Download the latest ARG-annot database (V3) +wget http://en.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/1424/arg-annot-nt-v3-march2017_doc.fasta -O argannot-refs.fna +awk '/>/{sub(">",">groot-db_ARGANNOT__")}1' argannot-refs.fna > tmp && mv tmp argannot-refs.fna + +# Download the latest ResFinder database +mkdir resfinder && cd $_ +wget https://bitbucket.org/genomicepidemiology/resfinder_db/get/dc33e2f9ec2c.zip -O resfinder.zip +unzip resfinder.zip +awk 'FNR==1{print ""}1' genomic*/*.fsa > resfinder-refs.fna +awk '/>/{sub(">",">groot-db_RESFINDER__")}1' resfinder-refs.fna > ../resfinder-refs.fna +cd .. && rm -r resfinder + +# Download the latest megres database +#mkdir megares && cd $_ +#wget --no-check-certificate -qO- https://megares.meglab.org/download/index.php | grep -Eo "megares_v.*/megares_database.*[0-9].fasta" | sort | uniq | tail -n 1 > megres-db-version +#megaresLink=$(sed 's/^/https:\/\/megares.meglab.org\/download\//g' megres-db-version) +#wget --no-check-certificate -O ../megares-refs.fna $megaresLink +#cd .. && rm -r megares + +# Create a reference file for the complete database +cat *.fna > all-args.fasta +seqkit rmdup --by-seq --ignore-case -j 8 -o all-args.dedup.fasta < all-args.fasta + +# Cluster total set and create groot-db +mkdir groot-db.90 && cd $_ +vsearch --cluster_size ../all-args.dedup.fasta --id 0.90 --msaout MSA.tmp +awk '!a[$0]++ {of="./cluster-" ++fc ".msa"; print $0 >> of ; close(of)}' RS= ORS="\n\n" MSA.tmp && rm MSA.tmp +date +%x_%H:%M:%S:%N | sed 's/\(:[0-9][0-9]\)[0-9]*$/\1/' > timestamp.txt +cd .. + +# Create the groot-core-db +mkdir groot-core-db.90 && cd $_ +cat ../*.fna > all-args.fasta +vsearch --cluster_size ../all-args.fasta --id 0.99 --msaout MSA.tmp +awk '!a[$0]++ {of="./cluster-" ++fc ".msa"; print $0 >> of ; close(of)}' RS= ORS="\n\n" MSA.tmp && rm MSA.tmp +for i in *.msa +do + seqNum=$(grep '>' ${i} | wc -l) + if [[ ${seqNum} > 3 ]]; then + grep '>' -m 1 ${i} | sed 's/>\*//' >> core-seqs.txt + fi + rm ${i} +done +cat all-args.fasta | seqkit grep -f core-seqs.txt > core-seqs.fna +vsearch --cluster_size core-seqs.fna --id 0.90 --msaout MSA.tmp +awk '!a[$0]++ {of="./cluster-" ++fc ".msa"; print $0 >> of ; close(of)}' RS= ORS="\n\n" MSA.tmp && rm MSA.tmp +date +%x_%H:%M:%S:%N | sed 's/\(:[0-9][0-9]\)[0-9]*$/\1/' > timestamp.txt +rm core-seq* all-arg* +cd .. + +# Finish up +mv groot* .. +cd .. && rm -r tmp +``` +
+ # Notes on the general approach Genes from ARG annotation outputs are mapped to ARO accessions using ARO annotation tables. ARO annotation tables are constructed using the RGI (Alcock et al., 2023) and manual curation. All databases except MEGARes v3.0 are handled as amino acid files, where all ARG sequences (coding sequences) in the databases are translated to amino acid form using BioPython (Cock et al., 2009). The amino acid files are processed by RGI using the ‘protein’ mode to map genes to the ARO. The ‘Original ID’ (gene name in ARG annotation database), ‘Best_Hit_ARO’ (gene name in CARD) and ‘ARO’ (ARO accession) columns from the RGI output are specifically chosen from the RGI output, with the ‘Best_Hit_ARO’ column renamed to ‘Gene Name in CARD’ , to form the automated annotation tables. Genes which were not given an ARO mapping by RGI are manually assigned an ARO accession. The manual curation and automated annotation tables are combined to produce ARO annotation tables. diff --git a/db_harmonisation/construct_groot_mappings.py b/db_harmonisation/construct_groot_mappings.py new file mode 100644 index 0000000..4c0c1f5 --- /dev/null +++ b/db_harmonisation/construct_groot_mappings.py @@ -0,0 +1,176 @@ +import pandas as pd +from argnorm.lib import get_aro_mapping_table +from Bio import SeqIO +from Bio.Seq import translate, reverse_complement, Seq +import subprocess +import requests +import os +from jug import TaskGenerator, barrier + +def download_file(url, ofile): + os.makedirs('dbs', exist_ok=True) + os.makedirs('mapping', exist_ok=True) + os.makedirs('manual_curation', exist_ok=True) + + with open(ofile, 'wb') as f: + r = requests.get(url, stream=True) + for chunk in r.iter_content(chunk_size=8192): + f.write(chunk) + return ofile + +@TaskGenerator +def get_groot_argannot_db(): + argannot_aro_mapping_table = get_aro_mapping_table('argannot') + argannot_aro_mapping_table.index = argannot_aro_mapping_table.index.str.lower() + + groot_argannot_genes = [] + groot_argannot_accessions = [] + preprocessed_argannot_refs = [] + + for i in list(argannot_aro_mapping_table.index): + gene_name = str(i).lower().split(':') + if not str(gene_name[2][0]).isnumeric() and not '-' in gene_name[2]: + preprocessed_argannot_refs.append(':'.join([gene_name[1], gene_name[3]])) + else: + preprocessed_argannot_refs.append(':'.join(i.split(':')[1:3])) + + argannot_aro_mapping_table.index = preprocessed_argannot_refs + download_file('https://www.mediterranee-infection.com/wp-content/uploads/2019/03/argannot-aa-v3-march2017.txt', 'dbs/argannot_groot_db.faa') + + with open('./dbs/argannot_groot_db.faa', 'r') as ifile, open('./manual_curation/groot_missing.fasta', 'w') as ofile: + for record in SeqIO.parse(ifile, 'fasta'): + gene = str(record.id).lower().split(':') + if not str(gene[2][0]).isnumeric() and not '-' in gene[2]: + id = ':'.join([gene[1], gene[3]]).lower() + else: + id = ':'.join(str(record.id).split(':')[1:3]).lower() + + if id in preprocessed_argannot_refs: + groot_argannot_genes.append(record.id) + groot_argannot_accessions.append(str(argannot_aro_mapping_table.loc[id, 'ARO']).replace('ARO:', '')) + else: + # These genes will be mapped through RGI as they aren't in the default argannot mappings + SeqIO.write(record, ofile, 'fasta') + argannot_groot_mapping = pd.DataFrame(groot_argannot_genes, columns=['Original ID']) + argannot_groot_mapping['ARO'] = groot_argannot_accessions + ofile = './mapping/argannot_groot_mapping.tsv' + argannot_groot_mapping.to_csv(ofile, sep='\t', index=False) + return ofile + +@TaskGenerator +def get_groot_resfinder_db(): + os.makedirs('resfinder', exist_ok=True) + download_file('https://bitbucket.org/genomicepidemiology/resfinder_db/get/dc33e2f9ec2c.zip', './resfinder/resfinder.zip') + + combine = """ + cd resfinder + unzip resfinder.zip + awk 'FNR==1{print ""}1' genomic*/*.fsa > resfinder_groot_db.fna + mv resfinder_groot_db.fna ../dbs/resfinder_groot_db.fna + cd .. && rm -rf resfinder + """ + subprocess.run(combine, shell=True, check=True) + + resfinder_aro_mapping_table = get_aro_mapping_table('resfinder') + groot_resfinder_genes = [] + groot_resfinder_accessions = [] + + with open('./dbs/resfinder_groot_db.fna', 'r') as ifile, open('./manual_curation/groot_missing.fasta', 'a') as ofile: + for record in SeqIO.parse(ifile, 'fasta'): + if str(record.id) in list(resfinder_aro_mapping_table.index): + groot_resfinder_genes.append(record.id) + groot_resfinder_accessions.append(str(resfinder_aro_mapping_table.loc[record.id, 'ARO']).replace('ARO:', '')) + else: + if record.seq.reverse_complement().translate().endswith('*')\ + and record.seq.reverse_complement().translate().count('*') == 1: + record.seq = Seq(str(reverse_complement(translate(record.seq))).replace('*', '')) + SeqIO.write(record, ofile, 'fasta') + else: + record.seq = Seq(str(translate(record.seq)).replace('*', '')) + SeqIO.write(record, ofile, 'fasta') + + resfinder_groot_mapping = pd.DataFrame(groot_resfinder_genes, columns=['Original ID']) + resfinder_groot_mapping['ARO'] = groot_resfinder_accessions + + ofile = './mapping/resfinder_groot_mapping.tsv' + resfinder_groot_mapping.to_csv(ofile, sep='\t', index=False) + return ofile + +@TaskGenerator +def get_groot_card_db(): + os.makedirs('card', exist_ok=True) + download_file('https://card.mcmaster.ca/latest/data', './card/data.tar.bz2') + subprocess.check_call('cd card && tar -xvf data.tar.bz2', shell=True) + os.rename('./card/nucleotide_fasta_protein_homolog_model.fasta', './dbs/card_groot_db.fna') + subprocess.check_call('rm -rf card', shell=True) + + card_genes = [] + card_accessions = [] + with open('./dbs/card_groot_db.fna', 'r') as ifile: + for record in SeqIO.parse(ifile, 'fasta'): + card_genes.append(str(record.id).split('|')[-1]) + card_accessions.append(str(record.id).split('|')[-2].replace('ARO:', '')) + + card_groot_mapping = pd.DataFrame(card_genes, columns=['Original ID']) + card_groot_mapping['ARO'] = card_accessions + + ofile = './mapping/card_groot_mapping.tsv' + card_groot_mapping.to_csv(ofile, sep='\t', index=False) + return ofile + +@TaskGenerator +def get_groot_missing(): + groot_missing_genes = [] + with open('./manual_curation/groot_missing.fasta', 'r') as ifile: + for record in SeqIO.parse(ifile, 'fasta'): + groot_missing_genes.append(record.id) + + subprocess.check_call([ + 'rgi', + 'main', + '-i', './manual_curation/groot_missing.fasta', + '-o', './mapping/groot_missing_mapping', + '-t', 'protein', + '-a', 'BLAST', + '--clean', + '--include_loose' + ]) + + missing_groot_mappings = pd.read_csv('./mapping/groot_missing_mapping.txt', sep='\t') + missing_groot_mappings['Original ID'] = missing_groot_mappings['ORF_ID'] + missing_groot_mappings_trim = missing_groot_mappings[['Original ID', 'ARO']] + ofile = './mapping/missing_groot_mapping.tsv' + missing_groot_mappings_trim.to_csv(ofile, sep='\t', index=False) + return ofile + +@TaskGenerator +def combine_groot_mappings(argannot_path, resfinder_path, card_path, missing_path): + argannot_groot_mapping = pd.read_csv(argannot_path, sep='\t') + resfinder_groot_mapping = pd.read_csv(resfinder_path, sep='\t') + card_groot_mapping = pd.read_csv(card_path, sep='\t') + missing_groot_mapping = pd.read_csv(missing_path, sep='\t') + + comb_groot_mapping = pd.concat([ + argannot_groot_mapping, + resfinder_groot_mapping, + card_groot_mapping, + missing_groot_mapping + ]).sort_values(by=['Original ID']) + comb_groot_mapping.to_csv('./mapping/groot_ARO_mapping.tsv', sep='\t', index=False) + + groot_missing_genes = [] + with open('./manual_curation/groot_missing.fasta', 'r') as ifile: + for record in SeqIO.parse(ifile, 'fasta'): + groot_missing_genes.append(record.id) + + groot_manual_curation = pd.DataFrame(list(set(groot_missing_genes) - set(comb_groot_mapping['Original ID'])), columns=['Original ID']) + groot_manual_curation.to_csv('./manual_curation/groot_curation.tsv', sep='\t', index=False) + +def get_groot_aro_mapping(): + argannot_input = get_groot_argannot_db() + resfinder_input = get_groot_resfinder_db() + card_input = get_groot_card_db() + missing_input = get_groot_missing() + combine_groot_mappings(argannot_input, resfinder_input, card_input, missing_input) + barrier() + os.rename('./mapping/groot_ARO_mapping.tsv', '../argnorm/data/groot_ARO_mapping.tsv') \ No newline at end of file diff --git a/db_harmonisation/crude_db_harmonisation.py b/db_harmonisation/crude_db_harmonisation.py index 25e2f3f..9950f50 100644 --- a/db_harmonisation/crude_db_harmonisation.py +++ b/db_harmonisation/crude_db_harmonisation.py @@ -8,6 +8,7 @@ from Bio import SeqIO from Bio.Seq import translate, Seq from construct_megares_mapping import construct_megares +from construct_groot_mappings import get_groot_aro_mapping @TaskGenerator def create_out_dirs(): @@ -127,4 +128,5 @@ def move_mappings_to_argnorm(aro_mapping): get_argannot_db() ]: move_mappings_to_argnorm(run_rgi(db)) -construct_megares() \ No newline at end of file +construct_megares() +get_groot_aro_mapping() \ No newline at end of file diff --git a/docs/api.md b/docs/api.md index cd728e2..ef0533d 100644 --- a/docs/api.md +++ b/docs/api.md @@ -11,6 +11,7 @@ A list of supported databases. #### Parameters * gene (str): The original ID of the gene as mentioned in source database. * database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg and sarg +* groot_ref_db (str, optional): name of reference database used by groot. Can be: groot-argannot, groot-resfinder, groot-card, groot-db, or groot-core-db #### Returns * pronto.term.Term: A pronto term with the ARO number of input gene. ARO number can be accessed using 'id' attribute and gene name can be accessed using 'name' attribute. @@ -20,15 +21,19 @@ A list of supported databases. #### Example ``` -# Mapping the `ARR-2_1_HQ141279` gene from the `resfinder` database to the ARO from argnorm.lib import map_to_aro + +# Mapping the `ARR-2_1_HQ141279` gene from the `resfinder` database to the ARO print(map_to_aro('ARR-2_1_HQ141279', 'resfinder')) + +# Mapping the `argannot~~~(Bla)cfxA4~~~AY769933:1-966` gene in `groot` using the `groot-argannot` reference database +print(map_to_aro('argannot~~~(Bla)cfxA4~~~AY769933:1-966', 'groot', 'groot-argannot')) ``` ### argnorm.lib.get_aro_mapping_table(): gets ARO mapping table for a specific database #### Parameters -* database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg and sarg +* database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg, sarg or groot #### Returns * pandas.DataFrame: A pandas dataframe with ARGs mapped to AROs. @@ -81,10 +86,10 @@ print(drugs_to_drug_classes(['ARO:0000030', 'ARO:0000051', 'ARO:0000069', 'ARO:3 Normalizers classes for specific tools which normalize ARG annotation outputs. Same functionality as CLI. All normalizers have 2 parameters: -* database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg and sarg. +* database (str): name of database. Can be: argannot, deeparg, megares, ncbi, resfinderfg, sarg, groot-db, groot-core-db, groot-card, groot-argannot, and groot-resfinder. * is_hamronized (bool, False by default): whether or not the ARG annotation output has been processed by the hamronization package. -> Note: the database parameter only needs to be specified for AbricateNormalizer. ncbi, deeparg, resfinder, sarg, megares, argannot, resfinderfg are the supported databases. +> Note: the database parameter only needs to be specified for AbricateNormalizer and GrootNormalizer. ncbi, deeparg, resfinder, sarg, megares, argannot, resfinderfg are the supported databases for AbricateNormalizer and groot-db, groot-core-db, groot-argannot, groot-resfinder, and groot-card are the supported databases for GrootNormalizer. Available normalizers: * argnorm.normalizers.ARGSOAPNormalizer @@ -92,6 +97,7 @@ Available normalizers: * argnorm.normalizers.ResFinderNormalizer * argnorm.normalizers.AMRFinderPlusNormalizer * argnorm.normalizers.AbricateNormalizer +* argnorm.normalizers.GrootNormalizer ### Methods diff --git a/docs/cli.md b/docs/cli.md index a8f1f44..429935a 100644 --- a/docs/cli.md +++ b/docs/cli.md @@ -147,4 +147,19 @@ argnorm resfinder -i examples/raw/resfinder.resfinder.reads.tsv -o outputs/raw/r argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.tsv argnorm amrfinderplus -i examples/hamronized/amrfinderplus.ncbi.orfs.tsv -o outputs/hamronized/amrfinderplus.ncbi.orfs.tsv +``` + +### GROOT +```bash +argnorm groot -i examples/raw/groot.argannot.tsv -o outputs/raw/groot.argannot.tsv --db groot-argannot +argnorm groot -i examples/raw/groot.resfinder.tsv -o outputs/raw/groot.resfinder.tsv --db groot-resfinder +argnorm groot -i examples/raw/groot.card.tsv -o outputs/raw/groot.card.tsv --db groot-card +argnorm groot -i examples/raw/groot.groot-db.tsv -o outputs/raw/groot.groot-db.tsv --db groot-db +argnorm groot -i examples/raw/groot.groot-core-db.tsv -o ouptuts/raw/groot.groot-core-db.tsv --db groot-core-db + +argnorm groot -i examples/hamronized/groot.argannot.tsv -o outputs/hamronized/groot.argannot.tsv --db groot-argannot --hamronized +argnorm groot -i examples/hamronized/groot.resfinder.tsv -o outputs/hamronized/groot.resfinder.tsv --db groot-resfinder --hamronized +argnorm groot -i examples/hamronized/groot.card.tsv -o outputs/hamronized/groot.card.tsv --db groot-card --hamronized +argnorm groot -i examples/hamronized/groot.groot-db.tsv -o outputs/hamronized/groot.groot-db.tsv --db groot-db --hamronized +argnorm groot -i examples/hamronized/groot.groot-core-db.tsv -o outputs/hamronized/groot.groot-core-db.tsv --db groot-core-db --hamronized ``` \ No newline at end of file diff --git a/examples/hamronized/groot.argannot.tsv b/examples/hamronized/groot.argannot.tsv index 0862378..7b21904 100644 --- a/examples/hamronized/groot.argannot.tsv +++ b/examples/hamronized/groot.argannot.tsv @@ -1,13 +1,13 @@ input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity -groot.argannot.tsv argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D groot v argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D groot v argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D groot v argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D groot v argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D groot v argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D groot v argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D groot v argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D groot v argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M groot v argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D groot v argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D groot v argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D groot v gene_presence_detected -groot.argannot.tsv argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D groot v argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D groot v gene_presence_detected +groot.argannot.tsv argannot~~~(Bla)cfiA9~~~AB087234:1-750 argannot~~~(Bla)cfiA9~~~AB087234:1-750 groot v argannot~~~(Bla)cfiA9~~~AB087234:1-750 groot v gene_presence_detected 79.0 750 +groot.argannot.tsv argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 groot v argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 groot v gene_presence_detected 315.0 1221 +groot.argannot.tsv argannot~~~(MLS)ErmF~~~M14730:241-1041 argannot~~~(MLS)ErmF~~~M14730:241-1041 groot v argannot~~~(MLS)ErmF~~~M14730:241-1041 groot v gene_presence_detected 321.0 801 +groot.argannot.tsv argannot~~~(AGly)Aph7~~~GG774704:686456-687373 argannot~~~(AGly)Aph7~~~GG774704:686456-687373 groot v argannot~~~(AGly)Aph7~~~GG774704:686456-687373 groot v gene_presence_detected 254.0 918 +groot.argannot.tsv argannot~~~(Bla)cfxA2~~~AF504910:1-966 argannot~~~(Bla)cfxA2~~~AF504910:1-966 groot v argannot~~~(Bla)cfxA2~~~AF504910:1-966 groot v gene_presence_detected 338.0 966 +groot.argannot.tsv argannot~~~(MLS)ErmB~~~M11180:714-1451 argannot~~~(MLS)ErmB~~~M11180:714-1451 groot v argannot~~~(MLS)ErmB~~~M11180:714-1451 groot v gene_presence_detected 178.0 738 +groot.argannot.tsv argannot~~~(Tet)TetQ~~~Z21523:362-2287 argannot~~~(Tet)TetQ~~~Z21523:362-2287 groot v argannot~~~(Tet)TetQ~~~Z21523:362-2287 groot v gene_presence_detected 539.0 1974 +groot.argannot.tsv argannot~~~(Bla)cfxA5~~~AY769934:28-993 argannot~~~(Bla)cfxA5~~~AY769934:28-993 groot v argannot~~~(Bla)cfxA5~~~AY769934:28-993 groot v gene_presence_detected 449.0 966 +groot.argannot.tsv argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 groot v argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 groot v gene_presence_detected 191.0 825 +groot.argannot.tsv argannot~~~(Tet)TetW~~~AJ222769:3687-5606 argannot~~~(Tet)TetW~~~AJ222769:3687-5606 groot v argannot~~~(Tet)TetW~~~AJ222769:3687-5606 groot v gene_presence_detected 203.0 1920 +groot.argannot.tsv argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 groot v argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 groot v gene_presence_detected 148.0 1920 +groot.argannot.tsv argannot~~~(Bla)cfxA4~~~AY769933:1-966 argannot~~~(Bla)cfxA4~~~AY769933:1-966 groot v argannot~~~(Bla)cfxA4~~~AY769933:1-966 groot v gene_presence_detected 450.0 966 diff --git a/examples/hamronized/groot.card.tsv b/examples/hamronized/groot.card.tsv index 258da1e..a5858a3 100644 --- a/examples/hamronized/groot.card.tsv +++ b/examples/hamronized/groot.card.tsv @@ -1,27 +1,27 @@ input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity -groot.card.tsv Mef(En2) Mef(En2).3004659.AF251288 groot v Mef(En2).3004659.AF251288.1.794-2000.5539 135 1206 11D599M16D568M12D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003410.U00096 groot v rrsB.3003410.U00096.4166659-4168200.3242 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003396.U00096 groot v rrsB.3003396.U00096.4166659-4168200.3233 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv Escherichia_coli_16S Escherichia_coli_16S.3003223.U00096 groot v Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv ErmB ErmB.3000375.AF242872 groot v ErmB.3000375.AF242872.1.2131-2878.5430 194 747 11D423M6D304M3D groot v gene_presence_detected -groot.card.tsv rrnB rrnB.3003411.U00096 groot v rrnB.3003411.U00096.4166659-4168200.3236 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003402.U00096 groot v rrsB.3003402.U00096.4166659-4168200.3235 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv rrnB rrnB.3003406.U00096 groot v rrnB.3003406.U00096.4166659-4168200.3237 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv tet(40) tet(40).3000567.AM419751 groot v tet(40).3000567.AM419751.14210-15431.5150 315 1221 156M7D1057M1D groot v gene_presence_detected -groot.card.tsv aadS aadS.3004683.M72415 groot v aadS.3004683.M72415.1.1120-1984.5568 199 864 364M2D496M2D groot v gene_presence_detected -groot.card.tsv CfxA4 CfxA4.3003005.AY769933 groot v CfxA4.3003005.AY769933.0-966.1592 450 966 960M6D groot v gene_presence_detected -groot.card.tsv rrnB rrnB.3003377.U00096 groot v rrnB.3003377.U00096.4166659-4168200.3239 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv OXA-347 OXA-347.3001777.JN086160 groot v OXA-347.3001777.JN086160.1582-2407.4583 191 825 11D812M1D1M groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003376.U00096 groot v rrsB.3003376.U00096.4166659-4168200.3240 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003408.U00096 groot v rrsB.3003408.U00096.4166659-4168200.3241 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv tetQ tetQ.3000191.Z21523 groot v tetQ.3000191.Z21523.0-1974.476 539 1974 1D1970M3D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003399.U00096 groot v rrsB.3003399.U00096.4166659-4168200.3232 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv tetW tetW.3000194.AJ222769 groot v tetW.3000194.AJ222769.3.3686-5606.5145 203 1920 2D1900M18D groot v gene_presence_detected -groot.card.tsv CfxA5 CfxA5.3003096.AY769934 groot v CfxA5.3003096.AY769934.27-993.1669 449 966 775M1D184M6D groot v gene_presence_detected -groot.card.tsv CfxA3 CfxA3.3003003.AF472622 groot v CfxA3.3003003.AF472622.52-1018.1514 519 966 960M6D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003405.U00096 groot v rrsB.3003405.U00096.4166659-4168200.3231 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv rrsH rrsH.3003372.U00096 groot v rrsH.3003372.U00096.223771-225312.3228 95 1542 6D1103M28D390M15D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003397.U00096 groot v rrsB.3003397.U00096.4166659-4168200.3230 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv ErmF ErmF.3000498.M17124 groot v ErmF.3000498.M17124.1181-1982.593 321 801 598M10D189M4D groot v gene_presence_detected -groot.card.tsv rrsB rrsB.3003403.U00096 groot v rrsB.3003403.U00096.4166659-4168200.3238 95 1542 6D1521M15D groot v gene_presence_detected -groot.card.tsv CfxA2 CfxA2.3003002.AF118110 groot v CfxA2.3003002.AF118110.1.71-1037.4470 450 966 960M6D groot v gene_presence_detected +groot.card.tsv Mef(En2) Mef(En2).3004659.AF251288 groot v Mef(En2).3004659.AF251288.1.794-2000.5539 groot v gene_presence_detected 135.0 1206 +groot.card.tsv rrsB rrsB.3003410.U00096 groot v rrsB.3003410.U00096.4166659-4168200.3242 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003396.U00096 groot v rrsB.3003396.U00096.4166659-4168200.3233 groot v gene_presence_detected 95.0 1542 +groot.card.tsv Escherichia_coli_16S Escherichia_coli_16S.3003223.U00096 groot v Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 groot v gene_presence_detected 95.0 1542 +groot.card.tsv ErmB ErmB.3000375.AF242872 groot v ErmB.3000375.AF242872.1.2131-2878.5430 groot v gene_presence_detected 194.0 747 +groot.card.tsv rrnB rrnB.3003411.U00096 groot v rrnB.3003411.U00096.4166659-4168200.3236 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003402.U00096 groot v rrsB.3003402.U00096.4166659-4168200.3235 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrnB rrnB.3003406.U00096 groot v rrnB.3003406.U00096.4166659-4168200.3237 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tet(40) tet(40).3000567.AM419751 groot v tet(40).3000567.AM419751.14210-15431.5150 groot v gene_presence_detected 315.0 1221 +groot.card.tsv aadS aadS.3004683.M72415 groot v aadS.3004683.M72415.1.1120-1984.5568 groot v gene_presence_detected 199.0 864 +groot.card.tsv CfxA4 CfxA4.3003005.AY769933 groot v CfxA4.3003005.AY769933.0-966.1592 groot v gene_presence_detected 450.0 966 +groot.card.tsv rrnB rrnB.3003377.U00096 groot v rrnB.3003377.U00096.4166659-4168200.3239 groot v gene_presence_detected 95.0 1542 +groot.card.tsv OXA-347 OXA-347.3001777.JN086160 groot v OXA-347.3001777.JN086160.1582-2407.4583 groot v gene_presence_detected 191.0 825 +groot.card.tsv rrsB rrsB.3003376.U00096 groot v rrsB.3003376.U00096.4166659-4168200.3240 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003408.U00096 groot v rrsB.3003408.U00096.4166659-4168200.3241 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tetQ tetQ.3000191.Z21523 groot v tetQ.3000191.Z21523.0-1974.476 groot v gene_presence_detected 539.0 1974 +groot.card.tsv rrsB rrsB.3003399.U00096 groot v rrsB.3003399.U00096.4166659-4168200.3232 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tetW tetW.3000194.AJ222769 groot v tetW.3000194.AJ222769.3.3686-5606.5145 groot v gene_presence_detected 203.0 1920 +groot.card.tsv CfxA5 CfxA5.3003096.AY769934 groot v CfxA5.3003096.AY769934.27-993.1669 groot v gene_presence_detected 449.0 966 +groot.card.tsv CfxA3 CfxA3.3003003.AF472622 groot v CfxA3.3003003.AF472622.52-1018.1514 groot v gene_presence_detected 519.0 966 +groot.card.tsv rrsB rrsB.3003405.U00096 groot v rrsB.3003405.U00096.4166659-4168200.3231 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsH rrsH.3003372.U00096 groot v rrsH.3003372.U00096.223771-225312.3228 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003397.U00096 groot v rrsB.3003397.U00096.4166659-4168200.3230 groot v gene_presence_detected 95.0 1542 +groot.card.tsv ErmF ErmF.3000498.M17124 groot v ErmF.3000498.M17124.1181-1982.593 groot v gene_presence_detected 321.0 801 +groot.card.tsv rrsB rrsB.3003403.U00096 groot v rrsB.3003403.U00096.4166659-4168200.3238 groot v gene_presence_detected 95.0 1542 +groot.card.tsv CfxA2 CfxA2.3003002.AF118110 groot v CfxA2.3003002.AF118110.1.71-1037.4470 groot v gene_presence_detected 450.0 966 diff --git a/examples/hamronized/groot.groot-core-db.tsv b/examples/hamronized/groot.groot-core-db.tsv index e935333..50a7e5f 100644 --- a/examples/hamronized/groot.groot-core-db.tsv +++ b/examples/hamronized/groot.groot-core-db.tsv @@ -1,7 +1,8 @@ input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity -groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 156M7D1057M1D groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 156M7D1057M1D groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 156M7D1057M1D groot v gene_presence_detected -groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D groot v gene_presence_detected -groot.groot-core-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot v gene_presence_detected -groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot v gene_presence_detected -groot.groot-core-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot v gene_presence_detected -groot.groot-core-db.tsv groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M groot v groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M groot v gene_presence_detected +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot v gene_presence_detected 1221.0 0 +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v gene_presence_detected 203.0 1920 +groot.groot-core-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v gene_presence_detected 271.0 1889 +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v gene_presence_detected 539.0 1974 +groot.groot-core-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v gene_presence_detected 321.0 801 +groot.groot-core-db.tsv groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot v groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot v gene_presence_detected 767.0 1920 + diff --git a/examples/hamronized/groot.groot-db.tsv b/examples/hamronized/groot.groot-db.tsv index b17e8e8..9e94970 100644 --- a/examples/hamronized/groot.groot-db.tsv +++ b/examples/hamronized/groot.groot-db.tsv @@ -1,45 +1,45 @@ input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity -groot.groot-db.tsv groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D groot v groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M groot v groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D groot v groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D groot v groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D groot v groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D groot v groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D groot v groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D groot v groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D groot v groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M groot v groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D groot v groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M groot v groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M groot v groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M groot v groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D groot v groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 912M6D groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 912M6D groot v groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 912M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D groot v groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D groot v groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D groot v groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D groot v groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D groot v groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D groot v groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D groot v groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D groot v groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D groot v groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D groot v groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 156M7D1058M groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 156M7D1058M groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 156M7D1058M groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D groot v groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D groot v groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D groot v groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M groot v groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D groot v groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D groot v groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D groot v groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M groot v groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D groot v groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D groot v groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D groot v gene_presence_detected -groot.groot-db.tsv groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D groot v groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M groot v groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M groot v gene_presence_detected -groot.groot-db.tsv groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M groot v groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M groot v gene_presence_detected -groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D groot v gene_presence_detected +groot.groot-db.tsv groot-db_RESFINDER__cfxA2_1_AF504914 groot-db_RESFINDER__cfxA2_1_AF504914 groot v groot-db_RESFINDER__cfxA2_1_AF504914 groot v gene_presence_detected 321.0 966 +groot.groot-db.tsv groot-db_RESFINDER__tet(40)_1_FJ158002 groot-db_RESFINDER__tet(40)_1_FJ158002 groot v groot-db_RESFINDER__tet(40)_1_FJ158002 groot v gene_presence_detected 411.0 1221 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot v groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot v gene_presence_detected 449.0 966 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_12_U18931 groot-db_RESFINDER__erm(B)_12_U18931 groot v groot-db_RESFINDER__erm(B)_12_U18931 groot v gene_presence_detected 238.0 738 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_7_AF368302 groot-db_RESFINDER__erm(B)_7_AF368302 groot v groot-db_RESFINDER__erm(B)_7_AF368302 groot v gene_presence_detected 201.0 711 +groot.groot-db.tsv groot-db_RESFINDER__cfxA3_1_AF472622 groot-db_RESFINDER__cfxA3_1_AF472622 groot v groot-db_RESFINDER__cfxA3_1_AF472622 groot v gene_presence_detected 519.0 966 +groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot v groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot v gene_presence_detected 178.0 738 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_1_JN899585 groot-db_RESFINDER__erm(B)_1_JN899585 groot v groot-db_RESFINDER__erm(B)_1_JN899585 groot v gene_presence_detected 214.0 738 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot v groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot v gene_presence_detected 450.0 966 +groot.groot-db.tsv groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot v groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot v gene_presence_detected 323.0 1222 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v gene_presence_detected 204.0 1920 +groot.groot-db.tsv groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot v groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot v gene_presence_detected 519.0 967 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_1_DQ060146 groot-db_RESFINDER__tet(W)_1_DQ060146 groot v groot-db_RESFINDER__tet(W)_1_DQ060146 groot v gene_presence_detected 202.0 1920 +groot.groot-db.tsv groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot v groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot v gene_presence_detected 196.0 1920 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v gene_presence_detected 271.0 1889 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_3_AJ427421 groot-db_RESFINDER__tet(W)_3_AJ427421 groot v groot-db_RESFINDER__tet(W)_3_AJ427421 groot v gene_presence_detected 200.0 1920 +groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_1_L33696 groot-db_RESFINDER__tet(Q)_1_L33696 groot v groot-db_RESFINDER__tet(Q)_1_L33696 groot v gene_presence_detected 1021.0 1926 +groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v gene_presence_detected 321.0 801 +groot.groot-db.tsv groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot v groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot v gene_presence_detected 918.0 0 +groot.groot-db.tsv groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot v groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot v gene_presence_detected 217.0 867 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot v groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot v gene_presence_detected 79.0 750 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_4_AM889121 groot-db_RESFINDER__tet(O/W)_4_AM889121 groot v groot-db_RESFINDER__tet(O/W)_4_AM889121 groot v gene_presence_detected 289.0 1889 +groot.groot-db.tsv groot-db_RESFINDER__erm(F)_3_M17808 groot-db_RESFINDER__erm(F)_3_M17808 groot v groot-db_RESFINDER__erm(F)_3_M17808 groot v gene_presence_detected 380.0 801 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_3_AM889120 groot-db_RESFINDER__tet(O/W)_3_AM889120 groot v groot-db_RESFINDER__tet(O/W)_3_AM889120 groot v gene_presence_detected 264.0 1889 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_9_AF299292 groot-db_RESFINDER__erm(B)_9_AF299292 groot v groot-db_RESFINDER__erm(B)_9_AF299292 groot v gene_presence_detected 191.0 738 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot v groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot v gene_presence_detected 148.0 1920 +groot.groot-db.tsv groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot v groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot v gene_presence_detected 452.0 967 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_6_AF242872 groot-db_RESFINDER__erm(B)_6_AF242872 groot v groot-db_RESFINDER__erm(B)_6_AF242872 groot v gene_presence_detected 192.0 747 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot v groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot v gene_presence_detected 338.0 966 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot v gene_presence_detected 1221.0 0 +groot.groot-db.tsv groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot v groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot v gene_presence_detected 192.0 748 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_11_M19270 groot-db_RESFINDER__erm(B)_11_M19270 groot v groot-db_RESFINDER__erm(B)_11_M19270 groot v gene_presence_detected 132.0 738 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_15_U48430 groot-db_RESFINDER__erm(B)_15_U48430 groot v groot-db_RESFINDER__erm(B)_15_U48430 groot v gene_presence_detected 159.0 753 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_4_FN396364 groot-db_RESFINDER__tet(W)_4_FN396364 groot v groot-db_RESFINDER__tet(W)_4_FN396364 groot v gene_presence_detected 216.0 1920 +groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_4_Z21523 groot-db_RESFINDER__tet(Q)_4_Z21523 groot v groot-db_RESFINDER__tet(Q)_4_Z21523 groot v gene_presence_detected 510.0 1926 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_2_AM889119 groot-db_RESFINDER__tet(O/W)_2_AM889119 groot v groot-db_RESFINDER__tet(O/W)_2_AM889119 groot v gene_presence_detected 232.0 1889 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_5_AM889122 groot-db_RESFINDER__tet(O/W)_5_AM889122 groot v groot-db_RESFINDER__tet(O/W)_5_AM889122 groot v gene_presence_detected 269.0 1889 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot v groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot v gene_presence_detected 191.0 825 +groot.groot-db.tsv groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot v groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot v gene_presence_detected 450.0 967 +groot.groot-db.tsv groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot v groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot v gene_presence_detected 191.0 826 +groot.groot-db.tsv groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot v groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot v gene_presence_detected 449.0 967 +groot.groot-db.tsv groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot v groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot v gene_presence_detected 767.0 1920 +groot.groot-db.tsv groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot v groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot v gene_presence_detected 718.0 1920 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v gene_presence_detected 539.0 1974 diff --git a/examples/hamronized/groot.resfinder.tsv b/examples/hamronized/groot.resfinder.tsv index 233c765..6843164 100644 --- a/examples/hamronized/groot.resfinder.tsv +++ b/examples/hamronized/groot.resfinder.tsv @@ -1,29 +1,29 @@ input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity -groot.resfinder.tsv cfiA9_1_AB087234 79 750 15D732M3D cfiA9_1_AB087234 79 750 15D732M3D groot v cfiA9_1_AB087234 79 750 15D732M3D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D groot v erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D groot v gene_presence_detected -groot.resfinder.tsv ant(6)-Ia_3_KF864551 217 867 852M15D ant(6)-Ia_3_KF864551 217 867 852M15D groot v ant(6)-Ia_3_KF864551 217 867 852M15D groot v gene_presence_detected -groot.resfinder.tsv tet(40)_3_AM419751 315 1221 156M7D1057M1D tet(40)_3_AM419751 315 1221 156M7D1057M1D groot v tet(40)_3_AM419751 315 1221 156M7D1057M1D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_15_U48430 159 753 4D567M2D159M21D erm(B)_15_U48430 159 753 4D567M2D159M21D groot v erm(B)_15_U48430 159 753 4D567M2D159M21D groot v gene_presence_detected -groot.resfinder.tsv blaOXA-347_1_JN086160 191 825 11D812M1D1M blaOXA-347_1_JN086160 191 825 11D812M1D1M groot v blaOXA-347_1_JN086160 191 825 11D812M1D1M groot v gene_presence_detected -groot.resfinder.tsv erm(B)_9_AF299292 191 738 4D732M2D erm(B)_9_AF299292 191 738 4D732M2D groot v erm(B)_9_AF299292 191 738 4D732M2D groot v gene_presence_detected -groot.resfinder.tsv tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D groot v tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D groot v gene_presence_detected -groot.resfinder.tsv cfxA2_1_AF504914 321 966 286M1D328M1D344M6D cfxA2_1_AF504914 321 966 286M1D328M1D344M6D groot v cfxA2_1_AF504914 321 966 286M1D328M1D344M6D groot v gene_presence_detected -groot.resfinder.tsv tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D groot v tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_6_AF242872 192 747 4D304M6D418M15D erm(B)_6_AF242872 192 747 4D304M6D418M15D groot v erm(B)_6_AF242872 192 747 4D304M6D418M15D groot v gene_presence_detected -groot.resfinder.tsv tet(40)_1_FJ158002 322 1221 1220M1D tet(40)_1_FJ158002 322 1221 1220M1D groot v tet(40)_1_FJ158002 322 1221 1220M1D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_1_JN899585 214 738 4D732M2D erm(B)_1_JN899585 214 738 4D732M2D groot v erm(B)_1_JN899585 214 738 4D732M2D groot v gene_presence_detected -groot.resfinder.tsv tet(32)_2_EF626943 148 1920 4D1897M19D tet(32)_2_EF626943 148 1920 4D1897M19D groot v tet(32)_2_EF626943 148 1920 4D1897M19D groot v gene_presence_detected -groot.resfinder.tsv cfxA3_1_AF472622 519 966 960M6D cfxA3_1_AF472622 519 966 960M6D groot v cfxA3_1_AF472622 519 966 960M6D groot v gene_presence_detected -groot.resfinder.tsv tet(Q)_4_Z21523 539 1974 1D1970M3D tet(Q)_4_Z21523 539 1974 1D1970M3D groot v tet(Q)_4_Z21523 539 1974 1D1970M3D groot v gene_presence_detected -groot.resfinder.tsv tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D groot v tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D groot v gene_presence_detected -groot.resfinder.tsv cfxA5_1_AY769934 449 966 775M1D184M6D cfxA5_1_AY769934 449 966 775M1D184M6D groot v cfxA5_1_AY769934 449 966 775M1D184M6D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_7_AF368302 201 711 4D705M2D erm(B)_7_AF368302 201 711 4D705M2D groot v erm(B)_7_AF368302 201 711 4D705M2D groot v gene_presence_detected -groot.resfinder.tsv erm(B)_10_U86375 178 738 4D732M2D erm(B)_10_U86375 178 738 4D732M2D groot v erm(B)_10_U86375 178 738 4D732M2D groot v gene_presence_detected -groot.resfinder.tsv cfxA4_1_AY769933 450 966 960M6D cfxA4_1_AY769933 450 966 960M6D groot v cfxA4_1_AY769933 450 966 960M6D groot v gene_presence_detected -groot.resfinder.tsv tetO_4_AIOQ01000025 767 1920 1783M5D132M tetO_4_AIOQ01000025 767 1920 1783M5D132M groot v tetO_4_AIOQ01000025 767 1920 1783M5D132M groot v gene_presence_detected -groot.resfinder.tsv erm(B)_12_U18931 238 738 4D732M2D erm(B)_12_U18931 238 738 4D732M2D groot v erm(B)_12_U18931 238 738 4D732M2D groot v gene_presence_detected -groot.resfinder.tsv tet(W)_4_AJ427422 203 1920 2D1900M18D tet(W)_4_AJ427422 203 1920 2D1900M18D groot v tet(W)_4_AJ427422 203 1920 2D1900M18D groot v gene_presence_detected -groot.resfinder.tsv erm(F)_2_M17124 321 801 598M10D189M4D erm(F)_2_M17124 321 801 598M10D189M4D groot v erm(F)_2_M17124 321 801 598M10D189M4D groot v gene_presence_detected -groot.resfinder.tsv tet(40)_2_FJ158002 409 1221 1220M1D tet(40)_2_FJ158002 409 1221 1220M1D groot v tet(40)_2_FJ158002 409 1221 1220M1D groot v gene_presence_detected -groot.resfinder.tsv erm(F)_3_M17808 380 801 797M4D erm(F)_3_M17808 380 801 797M4D groot v erm(F)_3_M17808 380 801 797M4D groot v gene_presence_detected -groot.resfinder.tsv tet(Q)_1_L33696 1021 1926 1684M1D237M4D tet(Q)_1_L33696 1021 1926 1684M1D237M4D groot v tet(Q)_1_L33696 1021 1926 1684M1D237M4D groot v gene_presence_detected +groot.resfinder.tsv cfiA9_1_AB087234 cfiA9_1_AB087234 groot v cfiA9_1_AB087234 groot v gene_presence_detected 79.0 750 +groot.resfinder.tsv erm(B)_11_M19270 erm(B)_11_M19270 groot v erm(B)_11_M19270 groot v gene_presence_detected 132.0 738 +groot.resfinder.tsv ant(6)-Ia_3_KF864551 ant(6)-Ia_3_KF864551 groot v ant(6)-Ia_3_KF864551 groot v gene_presence_detected 217.0 867 +groot.resfinder.tsv tet(40)_3_AM419751 tet(40)_3_AM419751 groot v tet(40)_3_AM419751 groot v gene_presence_detected 315.0 1221 +groot.resfinder.tsv erm(B)_15_U48430 erm(B)_15_U48430 groot v erm(B)_15_U48430 groot v gene_presence_detected 159.0 753 +groot.resfinder.tsv blaOXA-347_1_JN086160 blaOXA-347_1_JN086160 groot v blaOXA-347_1_JN086160 groot v gene_presence_detected 191.0 825 +groot.resfinder.tsv erm(B)_9_AF299292 erm(B)_9_AF299292 groot v erm(B)_9_AF299292 groot v gene_presence_detected 191.0 738 +groot.resfinder.tsv tet(W)_1_DQ060146 tet(W)_1_DQ060146 groot v tet(W)_1_DQ060146 groot v gene_presence_detected 201.0 1920 +groot.resfinder.tsv cfxA2_1_AF504914 cfxA2_1_AF504914 groot v cfxA2_1_AF504914 groot v gene_presence_detected 321.0 966 +groot.resfinder.tsv tet(W)_5_AJ427421 tet(W)_5_AJ427421 groot v tet(W)_5_AJ427421 groot v gene_presence_detected 199.0 1920 +groot.resfinder.tsv erm(B)_6_AF242872 erm(B)_6_AF242872 groot v erm(B)_6_AF242872 groot v gene_presence_detected 192.0 747 +groot.resfinder.tsv tet(40)_1_FJ158002 tet(40)_1_FJ158002 groot v tet(40)_1_FJ158002 groot v gene_presence_detected 322.0 1221 +groot.resfinder.tsv erm(B)_1_JN899585 erm(B)_1_JN899585 groot v erm(B)_1_JN899585 groot v gene_presence_detected 214.0 738 +groot.resfinder.tsv tet(32)_2_EF626943 tet(32)_2_EF626943 groot v tet(32)_2_EF626943 groot v gene_presence_detected 148.0 1920 +groot.resfinder.tsv cfxA3_1_AF472622 cfxA3_1_AF472622 groot v cfxA3_1_AF472622 groot v gene_presence_detected 519.0 966 +groot.resfinder.tsv tet(Q)_4_Z21523 tet(Q)_4_Z21523 groot v tet(Q)_4_Z21523 groot v gene_presence_detected 539.0 1974 +groot.resfinder.tsv tet(W)_6_FN396364 tet(W)_6_FN396364 groot v tet(W)_6_FN396364 groot v gene_presence_detected 215.0 1920 +groot.resfinder.tsv cfxA5_1_AY769934 cfxA5_1_AY769934 groot v cfxA5_1_AY769934 groot v gene_presence_detected 449.0 966 +groot.resfinder.tsv erm(B)_7_AF368302 erm(B)_7_AF368302 groot v erm(B)_7_AF368302 groot v gene_presence_detected 201.0 711 +groot.resfinder.tsv erm(B)_10_U86375 erm(B)_10_U86375 groot v erm(B)_10_U86375 groot v gene_presence_detected 178.0 738 +groot.resfinder.tsv cfxA4_1_AY769933 cfxA4_1_AY769933 groot v cfxA4_1_AY769933 groot v gene_presence_detected 450.0 966 +groot.resfinder.tsv tetO_4_AIOQ01000025 tetO_4_AIOQ01000025 groot v tetO_4_AIOQ01000025 groot v gene_presence_detected 767.0 1920 +groot.resfinder.tsv erm(B)_12_U18931 erm(B)_12_U18931 groot v erm(B)_12_U18931 groot v gene_presence_detected 238.0 738 +groot.resfinder.tsv tet(W)_4_AJ427422 tet(W)_4_AJ427422 groot v tet(W)_4_AJ427422 groot v gene_presence_detected 203.0 1920 +groot.resfinder.tsv erm(F)_2_M17124 erm(F)_2_M17124 groot v erm(F)_2_M17124 groot v gene_presence_detected 321.0 801 +groot.resfinder.tsv tet(40)_2_FJ158002 tet(40)_2_FJ158002 groot v tet(40)_2_FJ158002 groot v gene_presence_detected 409.0 1221 +groot.resfinder.tsv erm(F)_3_M17808 erm(F)_3_M17808 groot v erm(F)_3_M17808 groot v gene_presence_detected 380.0 801 +groot.resfinder.tsv tet(Q)_1_L33696 tet(Q)_1_L33696 groot v tet(Q)_1_L33696 groot v gene_presence_detected 1021.0 1926 \ No newline at end of file diff --git a/examples/raw/groot.argannot.tsv b/examples/raw/groot.argannot.tsv index c884c1f..fe321f0 100644 --- a/examples/raw/groot.argannot.tsv +++ b/examples/raw/groot.argannot.tsv @@ -1,12 +1,12 @@ -argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D -argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D -argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D -argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D -argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D -argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D -argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D -argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D -argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M -argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D -argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D -argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D \ No newline at end of file +argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D +argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D +argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D +argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D +argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D +argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D +argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D +argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D +argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M +argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D +argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D +argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D diff --git a/examples/raw/groot.card.tsv b/examples/raw/groot.card.tsv index acf02c1..aabad94 100644 --- a/examples/raw/groot.card.tsv +++ b/examples/raw/groot.card.tsv @@ -1,26 +1,26 @@ -Mef(En2).3004659.AF251288.1.794-2000.5539 135 1206 11D599M16D568M12D -rrsB.3003410.U00096.4166659-4168200.3242 95 1542 6D1521M15D -rrsB.3003396.U00096.4166659-4168200.3233 95 1542 6D1521M15D -Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 95 1542 6D1521M15D -ErmB.3000375.AF242872.1.2131-2878.5430 194 747 11D423M6D304M3D -rrnB.3003411.U00096.4166659-4168200.3236 95 1542 6D1521M15D -rrsB.3003402.U00096.4166659-4168200.3235 95 1542 6D1521M15D -rrnB.3003406.U00096.4166659-4168200.3237 95 1542 6D1521M15D -tet(40).3000567.AM419751.14210-15431.5150 315 1221 156M7D1057M1D -aadS.3004683.M72415.1.1120-1984.5568 199 864 364M2D496M2D -CfxA4.3003005.AY769933.0-966.1592 450 966 960M6D -rrnB.3003377.U00096.4166659-4168200.3239 95 1542 6D1521M15D -OXA-347.3001777.JN086160.1582-2407.4583 191 825 11D812M1D1M -rrsB.3003376.U00096.4166659-4168200.3240 95 1542 6D1521M15D -rrsB.3003408.U00096.4166659-4168200.3241 95 1542 6D1521M15D -tetQ.3000191.Z21523.0-1974.476 539 1974 1D1970M3D -rrsB.3003399.U00096.4166659-4168200.3232 95 1542 6D1521M15D -tetW.3000194.AJ222769.3.3686-5606.5145 203 1920 2D1900M18D -CfxA5.3003096.AY769934.27-993.1669 449 966 775M1D184M6D -CfxA3.3003003.AF472622.52-1018.1514 519 966 960M6D -rrsB.3003405.U00096.4166659-4168200.3231 95 1542 6D1521M15D -rrsH.3003372.U00096.223771-225312.3228 95 1542 6D1103M28D390M15D -rrsB.3003397.U00096.4166659-4168200.3230 95 1542 6D1521M15D -ErmF.3000498.M17124.1181-1982.593 321 801 598M10D189M4D -rrsB.3003403.U00096.4166659-4168200.3238 95 1542 6D1521M15D -CfxA2.3003002.AF118110.1.71-1037.4470 450 966 960M6D \ No newline at end of file +Mef(En2).3004659.AF251288.1.794-2000.5539 135 1206 11D599M16D568M12D +rrsB.3003410.U00096.4166659-4168200.3242 95 1542 6D1521M15D +rrsB.3003396.U00096.4166659-4168200.3233 95 1542 6D1521M15D +Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 95 1542 6D1521M15D +ErmB.3000375.AF242872.1.2131-2878.5430 194 747 11D423M6D304M3D +rrnB.3003411.U00096.4166659-4168200.3236 95 1542 6D1521M15D +rrsB.3003402.U00096.4166659-4168200.3235 95 1542 6D1521M15D +rrnB.3003406.U00096.4166659-4168200.3237 95 1542 6D1521M15D +tet(40).3000567.AM419751.14210-15431.5150 315 1221 156M7D1057M1D +aadS.3004683.M72415.1.1120-1984.5568 199 864 364M2D496M2D +CfxA4.3003005.AY769933.0-966.1592 450 966 960M6D +rrnB.3003377.U00096.4166659-4168200.3239 95 1542 6D1521M15D +OXA-347.3001777.JN086160.1582-2407.4583 191 825 11D812M1D1M +rrsB.3003376.U00096.4166659-4168200.3240 95 1542 6D1521M15D +rrsB.3003408.U00096.4166659-4168200.3241 95 1542 6D1521M15D +tetQ.3000191.Z21523.0-1974.476 539 1974 1D1970M3D +rrsB.3003399.U00096.4166659-4168200.3232 95 1542 6D1521M15D +tetW.3000194.AJ222769.3.3686-5606.5145 203 1920 2D1900M18D +CfxA5.3003096.AY769934.27-993.1669 449 966 775M1D184M6D +CfxA3.3003003.AF472622.52-1018.1514 519 966 960M6D +rrsB.3003405.U00096.4166659-4168200.3231 95 1542 6D1521M15D +rrsH.3003372.U00096.223771-225312.3228 95 1542 6D1103M28D390M15D +rrsB.3003397.U00096.4166659-4168200.3230 95 1542 6D1521M15D +ErmF.3000498.M17124.1181-1982.593 321 801 598M10D189M4D +rrsB.3003403.U00096.4166659-4168200.3238 95 1542 6D1521M15D +CfxA2.3003002.AF118110.1.71-1037.4470 450 966 960M6D diff --git a/examples/raw/groot.groot-core-db.tsv b/examples/raw/groot.groot-core-db.tsv index 67b2eb1..3abc642 100644 --- a/examples/raw/groot.groot-core-db.tsv +++ b/examples/raw/groot.groot-core-db.tsv @@ -1,6 +1,6 @@ -groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 156M7D1057M1D -groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D -groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D -groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D -groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D -groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M \ No newline at end of file +groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 0 156M7D1057M1D +groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D +groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D +groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D +groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D +groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M diff --git a/examples/raw/groot.groot-db.tsv b/examples/raw/groot.groot-db.tsv index 4e7224d..cec1a52 100644 --- a/examples/raw/groot.groot-db.tsv +++ b/examples/raw/groot.groot-db.tsv @@ -1,44 +1,44 @@ -groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D -groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M -groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D -groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D -groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D -groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D -groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D -groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D -groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D -groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M -groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M -groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D -groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M -groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M -groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D -groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M -groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D -groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D -groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 912M6D -groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D -groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D -groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D -groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D -groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D -groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D -groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D -groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D -groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D -groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D -groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 156M7D1058M -groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D -groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D -groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D -groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M -groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D -groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D -groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D -groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M -groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D -groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D -groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D -groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M -groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M -groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D \ No newline at end of file +groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D +groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M +groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D +groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D +groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D +groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D +groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D +groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D +groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D +groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M +groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M +groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D +groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M +groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M +groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D +groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M +groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D +groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D +groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 0 912M6D +groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D +groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D +groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D +groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D +groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D +groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D +groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D +groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D +groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D +groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D +groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 0 156M7D1058M +groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D +groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D +groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D +groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M +groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D +groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D +groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D +groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M +groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D +groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D +groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D +groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M +groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M +groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D diff --git a/examples/raw/groot.resfinder.tsv b/examples/raw/groot.resfinder.tsv index 6c9fa0a..bbedda2 100644 --- a/examples/raw/groot.resfinder.tsv +++ b/examples/raw/groot.resfinder.tsv @@ -1,28 +1,28 @@ -cfiA9_1_AB087234 79 750 15D732M3D -erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D -ant(6)-Ia_3_KF864551 217 867 852M15D -tet(40)_3_AM419751 315 1221 156M7D1057M1D -erm(B)_15_U48430 159 753 4D567M2D159M21D -blaOXA-347_1_JN086160 191 825 11D812M1D1M -erm(B)_9_AF299292 191 738 4D732M2D -tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D -cfxA2_1_AF504914 321 966 286M1D328M1D344M6D -tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D -erm(B)_6_AF242872 192 747 4D304M6D418M15D -tet(40)_1_FJ158002 322 1221 1220M1D -erm(B)_1_JN899585 214 738 4D732M2D -tet(32)_2_EF626943 148 1920 4D1897M19D -cfxA3_1_AF472622 519 966 960M6D -tet(Q)_4_Z21523 539 1974 1D1970M3D -tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D -cfxA5_1_AY769934 449 966 775M1D184M6D -erm(B)_7_AF368302 201 711 4D705M2D -erm(B)_10_U86375 178 738 4D732M2D -cfxA4_1_AY769933 450 966 960M6D -tetO_4_AIOQ01000025 767 1920 1783M5D132M -erm(B)_12_U18931 238 738 4D732M2D -tet(W)_4_AJ427422 203 1920 2D1900M18D -erm(F)_2_M17124 321 801 598M10D189M4D -tet(40)_2_FJ158002 409 1221 1220M1D -erm(F)_3_M17808 380 801 797M4D -tet(Q)_1_L33696 1021 1926 1684M1D237M4D \ No newline at end of file +cfiA9_1_AB087234 79 750 15D732M3D +erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D +ant(6)-Ia_3_KF864551 217 867 852M15D +tet(40)_3_AM419751 315 1221 156M7D1057M1D +erm(B)_15_U48430 159 753 4D567M2D159M21D +blaOXA-347_1_JN086160 191 825 11D812M1D1M +erm(B)_9_AF299292 191 738 4D732M2D +tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D +cfxA2_1_AF504914 321 966 286M1D328M1D344M6D +tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D +erm(B)_6_AF242872 192 747 4D304M6D418M15D +tet(40)_1_FJ158002 322 1221 1220M1D +erm(B)_1_JN899585 214 738 4D732M2D +tet(32)_2_EF626943 148 1920 4D1897M19D +cfxA3_1_AF472622 519 966 960M6D +tet(Q)_4_Z21523 539 1974 1D1970M3D +tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D +cfxA5_1_AY769934 449 966 775M1D184M6D +erm(B)_7_AF368302 201 711 4D705M2D +erm(B)_10_U86375 178 738 4D732M2D +cfxA4_1_AY769933 450 966 960M6D +tetO_4_AIOQ01000025 767 1920 1783M5D132M +erm(B)_12_U18931 238 738 4D732M2D +tet(W)_4_AJ427422 203 1920 2D1900M18D +erm(F)_2_M17124 321 801 598M10D189M4D +tet(40)_2_FJ158002 409 1221 1220M1D +erm(F)_3_M17808 380 801 797M4D +tet(Q)_1_L33696 1021 1926 1684M1D237M4D diff --git a/integration_tests/run_argnorm.py b/integration_tests/run_argnorm.py index 207bf0c..ef0aff5 100644 --- a/integration_tests/run_argnorm.py +++ b/integration_tests/run_argnorm.py @@ -16,7 +16,7 @@ def run_cli_test(tool, file, folder, db=None): if folder == 'hamronized': command.append('--hamronized') - if tool == 'abricate': + if tool in ['abricate', 'groot']: command += ['--db', db] subprocess.check_call(command) @@ -33,6 +33,11 @@ def run_cli_test(tool, file, folder, db=None): run_cli_test('amrfinderplus', 'amrfinderplus.ncbi.orfs.tsv', folder) run_cli_test('resfinder', 'resfinder.resfinder.reads.tsv', folder) run_cli_test('resfinder', 'resfinder.resfinder.orfs.tsv', folder) + for db in ['argannot', 'card', 'groot-core-db', 'groot-db', 'resfinder']: + database = db + if not 'groot' in db: + database = f'groot-{db}' + run_cli_test('groot', f'groot.{db}.tsv', folder, database) for db in ['ARGANNOT', 'argannot', 'MEGAres', 'megares', 'ncbi', 'resfinder', 'resfinderfg']: file = f'abricate.{db.lower()}.tsv' diff --git a/outputs/hamronized/groot.argannot.tsv b/outputs/hamronized/groot.argannot.tsv new file mode 100644 index 0000000..2ac3d92 --- /dev/null +++ b/outputs/hamronized/groot.argannot.tsv @@ -0,0 +1,13 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity ARO confers_resistance_to resistance_to_drug_classes +groot.argannot.tsv argannot~~~(Bla)cfiA9~~~AB087234:1-750 argannot~~~(Bla)cfiA9~~~AB087234:1-750 groot v argannot~~~(Bla)cfiA9~~~AB087234:1-750 groot v gene_presence_detected 79.0 750 ARO:3006921 ARO:0000020 ARO:3000007 +groot.argannot.tsv argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 groot v argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 groot v gene_presence_detected 315.0 1221 ARO:3000567 ARO:0000051 ARO:3000050 +groot.argannot.tsv argannot~~~(MLS)ErmF~~~M14730:241-1041 argannot~~~(MLS)ErmF~~~M14730:241-1041 groot v argannot~~~(MLS)ErmF~~~M14730:241-1041 groot v gene_presence_detected 321.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.argannot.tsv argannot~~~(AGly)Aph7~~~GG774704:686456-687373 argannot~~~(AGly)Aph7~~~GG774704:686456-687373 groot v argannot~~~(AGly)Aph7~~~GG774704:686456-687373 groot v gene_presence_detected 254.0 918 ARO:3002655 ARO:3000214 ARO:0000016 +groot.argannot.tsv argannot~~~(Bla)cfxA2~~~AF504910:1-966 argannot~~~(Bla)cfxA2~~~AF504910:1-966 groot v argannot~~~(Bla)cfxA2~~~AF504910:1-966 groot v gene_presence_detected 338.0 966 ARO:3003002 ARO:0000044 ARO:3000007 +groot.argannot.tsv argannot~~~(MLS)ErmB~~~M11180:714-1451 argannot~~~(MLS)ErmB~~~M11180:714-1451 groot v argannot~~~(MLS)ErmB~~~M11180:714-1451 groot v gene_presence_detected 178.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.argannot.tsv argannot~~~(Tet)TetQ~~~Z21523:362-2287 argannot~~~(Tet)TetQ~~~Z21523:362-2287 groot v argannot~~~(Tet)TetQ~~~Z21523:362-2287 groot v gene_presence_detected 539.0 1974 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.argannot.tsv argannot~~~(Bla)cfxA5~~~AY769934:28-993 argannot~~~(Bla)cfxA5~~~AY769934:28-993 groot v argannot~~~(Bla)cfxA5~~~AY769934:28-993 groot v gene_presence_detected 449.0 966 ARO:3003096 ARO:0000044 ARO:3000007 +groot.argannot.tsv argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 groot v argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 groot v gene_presence_detected 191.0 825 ARO:3001777 ARO:0000056 ARO:3000007 +groot.argannot.tsv argannot~~~(Tet)TetW~~~AJ222769:3687-5606 argannot~~~(Tet)TetW~~~AJ222769:3687-5606 groot v argannot~~~(Tet)TetW~~~AJ222769:3687-5606 groot v gene_presence_detected 203.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.argannot.tsv argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 groot v argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 groot v gene_presence_detected 148.0 1920 ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.argannot.tsv argannot~~~(Bla)cfxA4~~~AY769933:1-966 argannot~~~(Bla)cfxA4~~~AY769933:1-966 groot v argannot~~~(Bla)cfxA4~~~AY769933:1-966 groot v gene_presence_detected 450.0 966 ARO:3003005 ARO:0000044 ARO:3000007 diff --git a/outputs/hamronized/groot.card.tsv b/outputs/hamronized/groot.card.tsv new file mode 100644 index 0000000..64fb85e --- /dev/null +++ b/outputs/hamronized/groot.card.tsv @@ -0,0 +1,27 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity ARO confers_resistance_to resistance_to_drug_classes +groot.card.tsv Mef(En2) Mef(En2).3004659.AF251288 groot v Mef(En2).3004659.AF251288.1.794-2000.5539 groot v gene_presence_detected 135.0 1206 ARO:3004659 ARO:0000046 ARO:0000017 +groot.card.tsv rrsB rrsB.3003410.U00096 groot v rrsB.3003410.U00096.4166659-4168200.3242 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003396.U00096 groot v rrsB.3003396.U00096.4166659-4168200.3233 groot v gene_presence_detected 95.0 1542 +groot.card.tsv Escherichia_coli_16S Escherichia_coli_16S.3003223.U00096 groot v Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 groot v gene_presence_detected 95.0 1542 +groot.card.tsv ErmB ErmB.3000375.AF242872 groot v ErmB.3000375.AF242872.1.2131-2878.5430 groot v gene_presence_detected 194.0 747 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.card.tsv rrnB rrnB.3003411.U00096 groot v rrnB.3003411.U00096.4166659-4168200.3236 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003402.U00096 groot v rrsB.3003402.U00096.4166659-4168200.3235 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrnB rrnB.3003406.U00096 groot v rrnB.3003406.U00096.4166659-4168200.3237 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tet(40) tet(40).3000567.AM419751 groot v tet(40).3000567.AM419751.14210-15431.5150 groot v gene_presence_detected 315.0 1221 ARO:3000567 ARO:0000051 ARO:3000050 +groot.card.tsv aadS aadS.3004683.M72415 groot v aadS.3004683.M72415.1.1120-1984.5568 groot v gene_presence_detected 199.0 864 ARO:3004683 ARO:0000040 ARO:0000016 +groot.card.tsv CfxA4 CfxA4.3003005.AY769933 groot v CfxA4.3003005.AY769933.0-966.1592 groot v gene_presence_detected 450.0 966 ARO:3003005 ARO:0000044 ARO:3000007 +groot.card.tsv rrnB rrnB.3003377.U00096 groot v rrnB.3003377.U00096.4166659-4168200.3239 groot v gene_presence_detected 95.0 1542 +groot.card.tsv OXA-347 OXA-347.3001777.JN086160 groot v OXA-347.3001777.JN086160.1582-2407.4583 groot v gene_presence_detected 191.0 825 ARO:3001777 ARO:0000056 ARO:3000007 +groot.card.tsv rrsB rrsB.3003376.U00096 groot v rrsB.3003376.U00096.4166659-4168200.3240 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003408.U00096 groot v rrsB.3003408.U00096.4166659-4168200.3241 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tetQ tetQ.3000191.Z21523 groot v tetQ.3000191.Z21523.0-1974.476 groot v gene_presence_detected 539.0 1974 +groot.card.tsv rrsB rrsB.3003399.U00096 groot v rrsB.3003399.U00096.4166659-4168200.3232 groot v gene_presence_detected 95.0 1542 +groot.card.tsv tetW tetW.3000194.AJ222769 groot v tetW.3000194.AJ222769.3.3686-5606.5145 groot v gene_presence_detected 203.0 1920 +groot.card.tsv CfxA5 CfxA5.3003096.AY769934 groot v CfxA5.3003096.AY769934.27-993.1669 groot v gene_presence_detected 449.0 966 ARO:3003096 ARO:0000044 ARO:3000007 +groot.card.tsv CfxA3 CfxA3.3003003.AF472622 groot v CfxA3.3003003.AF472622.52-1018.1514 groot v gene_presence_detected 519.0 966 ARO:3003003 ARO:0000044 ARO:3000007 +groot.card.tsv rrsB rrsB.3003405.U00096 groot v rrsB.3003405.U00096.4166659-4168200.3231 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsH rrsH.3003372.U00096 groot v rrsH.3003372.U00096.223771-225312.3228 groot v gene_presence_detected 95.0 1542 +groot.card.tsv rrsB rrsB.3003397.U00096 groot v rrsB.3003397.U00096.4166659-4168200.3230 groot v gene_presence_detected 95.0 1542 +groot.card.tsv ErmF ErmF.3000498.M17124 groot v ErmF.3000498.M17124.1181-1982.593 groot v gene_presence_detected 321.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.card.tsv rrsB rrsB.3003403.U00096 groot v rrsB.3003403.U00096.4166659-4168200.3238 groot v gene_presence_detected 95.0 1542 +groot.card.tsv CfxA2 CfxA2.3003002.AF118110 groot v CfxA2.3003002.AF118110.1.71-1037.4470 groot v gene_presence_detected 450.0 966 ARO:3003002 ARO:0000044 ARO:3000007 diff --git a/outputs/hamronized/groot.groot-core-db.tsv b/outputs/hamronized/groot.groot-core-db.tsv new file mode 100644 index 0000000..f4d18eb --- /dev/null +++ b/outputs/hamronized/groot.groot-core-db.tsv @@ -0,0 +1,7 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity ARO confers_resistance_to resistance_to_drug_classes +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 groot v gene_presence_detected 1221.0 0 +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v gene_presence_detected 203.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-core-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v gene_presence_detected 271.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-core-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v gene_presence_detected 539.0 1974 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-core-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v gene_presence_detected 321.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-core-db.tsv groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot v groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 groot v gene_presence_detected 767.0 1920 ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/outputs/hamronized/groot.groot-db.tsv b/outputs/hamronized/groot.groot-db.tsv new file mode 100644 index 0000000..73a0709 --- /dev/null +++ b/outputs/hamronized/groot.groot-db.tsv @@ -0,0 +1,45 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity ARO confers_resistance_to resistance_to_drug_classes +groot.groot-db.tsv groot-db_RESFINDER__cfxA2_1_AF504914 groot-db_RESFINDER__cfxA2_1_AF504914 groot v groot-db_RESFINDER__cfxA2_1_AF504914 groot v gene_presence_detected 321.0 966 ARO:3003002 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__tet(40)_1_FJ158002 groot-db_RESFINDER__tet(40)_1_FJ158002 groot v groot-db_RESFINDER__tet(40)_1_FJ158002 groot v gene_presence_detected 411.0 1221 ARO:3000567 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot v groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 groot v gene_presence_detected 449.0 966 ARO:3003096 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_12_U18931 groot-db_RESFINDER__erm(B)_12_U18931 groot v groot-db_RESFINDER__erm(B)_12_U18931 groot v gene_presence_detected 238.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_7_AF368302 groot-db_RESFINDER__erm(B)_7_AF368302 groot v groot-db_RESFINDER__erm(B)_7_AF368302 groot v gene_presence_detected 201.0 711 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__cfxA3_1_AF472622 groot-db_RESFINDER__cfxA3_1_AF472622 groot v groot-db_RESFINDER__cfxA3_1_AF472622 groot v gene_presence_detected 519.0 966 ARO:3003003 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot v groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 groot v gene_presence_detected 178.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_1_JN899585 groot-db_RESFINDER__erm(B)_1_JN899585 groot v groot-db_RESFINDER__erm(B)_1_JN899585 groot v gene_presence_detected 214.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot v groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 groot v gene_presence_detected 450.0 966 ARO:3003005 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot v groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) groot v gene_presence_detected 323.0 1222 ARO:3000567 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 groot v gene_presence_detected 204.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot v groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 groot v gene_presence_detected 519.0 967 ARO:3003003 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_1_DQ060146 groot-db_RESFINDER__tet(W)_1_DQ060146 groot v groot-db_RESFINDER__tet(W)_1_DQ060146 groot v gene_presence_detected 202.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot v groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW groot v gene_presence_detected 196.0 1920 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_1_AM889118 groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v groot-db_RESFINDER__tet(O/W)_1_AM889118 groot v gene_presence_detected 271.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_3_AJ427421 groot-db_RESFINDER__tet(W)_3_AJ427421 groot v groot-db_RESFINDER__tet(W)_3_AJ427421 groot v gene_presence_detected 200.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_1_L33696 groot-db_RESFINDER__tet(Q)_1_L33696 groot v groot-db_RESFINDER__tet(Q)_1_L33696 groot v gene_presence_detected 1021.0 1926 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 groot v gene_presence_detected 321.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot v groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 groot v gene_presence_detected 918.0 0 +groot.groot-db.tsv groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot v groot-db_RESFINDER__ant(6)-Ia_3_KF864551 groot v gene_presence_detected 217.0 867 ARO:3002629 ARO:0000040 ARO:0000016 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot v groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 groot v gene_presence_detected 79.0 750 ARO:3006921 ARO:0000020 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_4_AM889121 groot-db_RESFINDER__tet(O/W)_4_AM889121 groot v groot-db_RESFINDER__tet(O/W)_4_AM889121 groot v gene_presence_detected 289.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__erm(F)_3_M17808 groot-db_RESFINDER__erm(F)_3_M17808 groot v groot-db_RESFINDER__erm(F)_3_M17808 groot v gene_presence_detected 380.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_3_AM889120 groot-db_RESFINDER__tet(O/W)_3_AM889120 groot v groot-db_RESFINDER__tet(O/W)_3_AM889120 groot v gene_presence_detected 264.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_9_AF299292 groot-db_RESFINDER__erm(B)_9_AF299292 groot v groot-db_RESFINDER__erm(B)_9_AF299292 groot v gene_presence_detected 191.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot v groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 groot v gene_presence_detected 148.0 1920 ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot v groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 groot v gene_presence_detected 452.0 967 ARO:3003002 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_6_AF242872 groot-db_RESFINDER__erm(B)_6_AF242872 groot v groot-db_RESFINDER__erm(B)_6_AF242872 groot v gene_presence_detected 192.0 747 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot v groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 groot v gene_presence_detected 338.0 966 ARO:3003002 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot v groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 groot v gene_presence_detected 1221.0 0 +groot.groot-db.tsv groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot v groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB groot v gene_presence_detected 192.0 748 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_11_M19270 groot-db_RESFINDER__erm(B)_11_M19270 groot v groot-db_RESFINDER__erm(B)_11_M19270 groot v gene_presence_detected 132.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__erm(B)_15_U48430 groot-db_RESFINDER__erm(B)_15_U48430 groot v groot-db_RESFINDER__erm(B)_15_U48430 groot v gene_presence_detected 159.0 753 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.groot-db.tsv groot-db_RESFINDER__tet(W)_4_FN396364 groot-db_RESFINDER__tet(W)_4_FN396364 groot v groot-db_RESFINDER__tet(W)_4_FN396364 groot v gene_presence_detected 216.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(Q)_4_Z21523 groot-db_RESFINDER__tet(Q)_4_Z21523 groot v groot-db_RESFINDER__tet(Q)_4_Z21523 groot v gene_presence_detected 510.0 1926 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_2_AM889119 groot-db_RESFINDER__tet(O/W)_2_AM889119 groot v groot-db_RESFINDER__tet(O/W)_2_AM889119 groot v gene_presence_detected 232.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(O/W)_5_AM889122 groot-db_RESFINDER__tet(O/W)_5_AM889122 groot v groot-db_RESFINDER__tet(O/W)_5_AM889122 groot v gene_presence_detected 269.0 1889 ARO:3007121 ARO:0000051 ARO:3000050 +groot.groot-db.tsv groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot v groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 groot v gene_presence_detected 191.0 825 ARO:3001777 ARO:0000056 ARO:3000007 +groot.groot-db.tsv groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot v groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 groot v gene_presence_detected 450.0 967 ARO:3003005 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot v groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 groot v gene_presence_detected 191.0 826 ARO:3001777 ARO:0000056 ARO:3000007 +groot.groot-db.tsv groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot v groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 groot v gene_presence_detected 449.0 967 ARO:3003096 ARO:0000044 ARO:3000007 +groot.groot-db.tsv groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot v groot-db_RESFINDER__tet(O)_4_AIOQ01000025 groot v gene_presence_detected 767.0 1920 ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot v groot-db_RESFINDER__tet(0/32/0)_7_FP929050 groot v gene_presence_detected 718.0 1920 ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.groot-db.tsv groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 groot v gene_presence_detected 539.0 1974 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/outputs/hamronized/groot.resfinder.tsv b/outputs/hamronized/groot.resfinder.tsv new file mode 100644 index 0000000..e1b096e --- /dev/null +++ b/outputs/hamronized/groot.resfinder.tsv @@ -0,0 +1,29 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity ARO confers_resistance_to resistance_to_drug_classes +groot.resfinder.tsv cfiA9_1_AB087234 cfiA9_1_AB087234 groot v cfiA9_1_AB087234 groot v gene_presence_detected 79.0 750 ARO:3006921 ARO:0000020 ARO:3000007 +groot.resfinder.tsv erm(B)_11_M19270 erm(B)_11_M19270 groot v erm(B)_11_M19270 groot v gene_presence_detected 132.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv ant(6)-Ia_3_KF864551 ant(6)-Ia_3_KF864551 groot v ant(6)-Ia_3_KF864551 groot v gene_presence_detected 217.0 867 ARO:3002629 ARO:0000040 ARO:0000016 +groot.resfinder.tsv tet(40)_3_AM419751 tet(40)_3_AM419751 groot v tet(40)_3_AM419751 groot v gene_presence_detected 315.0 1221 +groot.resfinder.tsv erm(B)_15_U48430 erm(B)_15_U48430 groot v erm(B)_15_U48430 groot v gene_presence_detected 159.0 753 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv blaOXA-347_1_JN086160 blaOXA-347_1_JN086160 groot v blaOXA-347_1_JN086160 groot v gene_presence_detected 191.0 825 ARO:3001777 ARO:0000056 ARO:3000007 +groot.resfinder.tsv erm(B)_9_AF299292 erm(B)_9_AF299292 groot v erm(B)_9_AF299292 groot v gene_presence_detected 191.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(W)_1_DQ060146 tet(W)_1_DQ060146 groot v tet(W)_1_DQ060146 groot v gene_presence_detected 201.0 1920 ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.resfinder.tsv cfxA2_1_AF504914 cfxA2_1_AF504914 groot v cfxA2_1_AF504914 groot v gene_presence_detected 321.0 966 ARO:3003002 ARO:0000044 ARO:3000007 +groot.resfinder.tsv tet(W)_5_AJ427421 tet(W)_5_AJ427421 groot v tet(W)_5_AJ427421 groot v gene_presence_detected 199.0 1920 +groot.resfinder.tsv erm(B)_6_AF242872 erm(B)_6_AF242872 groot v erm(B)_6_AF242872 groot v gene_presence_detected 192.0 747 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(40)_1_FJ158002 tet(40)_1_FJ158002 groot v tet(40)_1_FJ158002 groot v gene_presence_detected 322.0 1221 ARO:3000567 ARO:0000051 ARO:3000050 +groot.resfinder.tsv erm(B)_1_JN899585 erm(B)_1_JN899585 groot v erm(B)_1_JN899585 groot v gene_presence_detected 214.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(32)_2_EF626943 tet(32)_2_EF626943 groot v tet(32)_2_EF626943 groot v gene_presence_detected 148.0 1920 ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.resfinder.tsv cfxA3_1_AF472622 cfxA3_1_AF472622 groot v cfxA3_1_AF472622 groot v gene_presence_detected 519.0 966 ARO:3003003 ARO:0000044 ARO:3000007 +groot.resfinder.tsv tet(Q)_4_Z21523 tet(Q)_4_Z21523 groot v tet(Q)_4_Z21523 groot v gene_presence_detected 539.0 1974 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot.resfinder.tsv tet(W)_6_FN396364 tet(W)_6_FN396364 groot v tet(W)_6_FN396364 groot v gene_presence_detected 215.0 1920 +groot.resfinder.tsv cfxA5_1_AY769934 cfxA5_1_AY769934 groot v cfxA5_1_AY769934 groot v gene_presence_detected 449.0 966 ARO:3003096 ARO:0000044 ARO:3000007 +groot.resfinder.tsv erm(B)_7_AF368302 erm(B)_7_AF368302 groot v erm(B)_7_AF368302 groot v gene_presence_detected 201.0 711 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv erm(B)_10_U86375 erm(B)_10_U86375 groot v erm(B)_10_U86375 groot v gene_presence_detected 178.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv cfxA4_1_AY769933 cfxA4_1_AY769933 groot v cfxA4_1_AY769933 groot v gene_presence_detected 450.0 966 ARO:3003005 ARO:0000044 ARO:3000007 +groot.resfinder.tsv tetO_4_AIOQ01000025 tetO_4_AIOQ01000025 groot v tetO_4_AIOQ01000025 groot v gene_presence_detected 767.0 1920 +groot.resfinder.tsv erm(B)_12_U18931 erm(B)_12_U18931 groot v erm(B)_12_U18931 groot v gene_presence_detected 238.0 738 ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(W)_4_AJ427422 tet(W)_4_AJ427422 groot v tet(W)_4_AJ427422 groot v gene_presence_detected 203.0 1920 +groot.resfinder.tsv erm(F)_2_M17124 erm(F)_2_M17124 groot v erm(F)_2_M17124 groot v gene_presence_detected 321.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(40)_2_FJ158002 tet(40)_2_FJ158002 groot v tet(40)_2_FJ158002 groot v gene_presence_detected 409.0 1221 +groot.resfinder.tsv erm(F)_3_M17808 erm(F)_3_M17808 groot v erm(F)_3_M17808 groot v gene_presence_detected 380.0 801 ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot.resfinder.tsv tet(Q)_1_L33696 tet(Q)_1_L33696 groot v tet(Q)_1_L33696 groot v gene_presence_detected 1021.0 1926 ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/outputs/raw/groot.argannot.tsv b/outputs/raw/groot.argannot.tsv new file mode 100644 index 0000000..034e690 --- /dev/null +++ b/outputs/raw/groot.argannot.tsv @@ -0,0 +1,13 @@ +0 1 2 3 ARO confers_resistance_to resistance_to_drug_classes +argannot~~~(Bla)cfiA9~~~AB087234:1-750 79 750 15D732M3D ARO:3006921 ARO:0000020 ARO:3000007 +argannot~~~(Tet)Tet-40~~~AM419751:14211-15431 315 1221 156M7D1057M1D ARO:3000567 ARO:0000051 ARO:3000050 +argannot~~~(MLS)ErmF~~~M14730:241-1041 321 801 598M10D189M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +argannot~~~(AGly)Aph7~~~GG774704:686456-687373 254 918 912M6D ARO:3002655 ARO:3000214 ARO:0000016 +argannot~~~(Bla)cfxA2~~~AF504910:1-966 338 966 101M1D401M2D455M6D ARO:3003002 ARO:0000044 ARO:3000007 +argannot~~~(MLS)ErmB~~~M11180:714-1451 178 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +argannot~~~(Tet)TetQ~~~Z21523:362-2287 539 1974 1D1970M3D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +argannot~~~(Bla)cfxA5~~~AY769934:28-993 449 966 775M1D184M6D ARO:3003096 ARO:0000044 ARO:3000007 +argannot~~~(Bla)OXA-347~~~JN086160:1583-2407 191 825 11D812M1D1M ARO:3001777 ARO:0000056 ARO:3000007 +argannot~~~(Tet)TetW~~~AJ222769:3687-5606 203 1920 2D1900M18D ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +argannot~~~(Tet)Tet-32~~~DQ647324:181-2100 148 1920 4D1897M19D ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +argannot~~~(Bla)cfxA4~~~AY769933:1-966 450 966 960M6D ARO:3003005 ARO:0000044 ARO:3000007 diff --git a/outputs/raw/groot.card.tsv b/outputs/raw/groot.card.tsv new file mode 100644 index 0000000..ecfd9a9 --- /dev/null +++ b/outputs/raw/groot.card.tsv @@ -0,0 +1,27 @@ +0 1 2 3 ARO confers_resistance_to resistance_to_drug_classes +Mef(En2).3004659.AF251288.1.794-2000.5539 135 1206 11D599M16D568M12D ARO:3004659 ARO:0000046 ARO:0000017 +rrsB.3003410.U00096.4166659-4168200.3242 95 1542 6D1521M15D +rrsB.3003396.U00096.4166659-4168200.3233 95 1542 6D1521M15D +Escherichia_coli_16S.3003223.U00096.4166659-4168200.3234 95 1542 6D1521M15D +ErmB.3000375.AF242872.1.2131-2878.5430 194 747 11D423M6D304M3D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +rrnB.3003411.U00096.4166659-4168200.3236 95 1542 6D1521M15D +rrsB.3003402.U00096.4166659-4168200.3235 95 1542 6D1521M15D +rrnB.3003406.U00096.4166659-4168200.3237 95 1542 6D1521M15D +tet(40).3000567.AM419751.14210-15431.5150 315 1221 156M7D1057M1D ARO:3000567 ARO:0000051 ARO:3000050 +aadS.3004683.M72415.1.1120-1984.5568 199 864 364M2D496M2D ARO:3004683 ARO:0000040 ARO:0000016 +CfxA4.3003005.AY769933.0-966.1592 450 966 960M6D ARO:3003005 ARO:0000044 ARO:3000007 +rrnB.3003377.U00096.4166659-4168200.3239 95 1542 6D1521M15D +OXA-347.3001777.JN086160.1582-2407.4583 191 825 11D812M1D1M ARO:3001777 ARO:0000056 ARO:3000007 +rrsB.3003376.U00096.4166659-4168200.3240 95 1542 6D1521M15D +rrsB.3003408.U00096.4166659-4168200.3241 95 1542 6D1521M15D +tetQ.3000191.Z21523.0-1974.476 539 1974 1D1970M3D +rrsB.3003399.U00096.4166659-4168200.3232 95 1542 6D1521M15D +tetW.3000194.AJ222769.3.3686-5606.5145 203 1920 2D1900M18D +CfxA5.3003096.AY769934.27-993.1669 449 966 775M1D184M6D ARO:3003096 ARO:0000044 ARO:3000007 +CfxA3.3003003.AF472622.52-1018.1514 519 966 960M6D ARO:3003003 ARO:0000044 ARO:3000007 +rrsB.3003405.U00096.4166659-4168200.3231 95 1542 6D1521M15D +rrsH.3003372.U00096.223771-225312.3228 95 1542 6D1103M28D390M15D +rrsB.3003397.U00096.4166659-4168200.3230 95 1542 6D1521M15D +ErmF.3000498.M17124.1181-1982.593 321 801 598M10D189M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +rrsB.3003403.U00096.4166659-4168200.3238 95 1542 6D1521M15D +CfxA2.3003002.AF118110.1.71-1037.4470 450 966 960M6D ARO:3003002 ARO:0000044 ARO:3000007 diff --git a/outputs/raw/groot.groot-core-db.tsv b/outputs/raw/groot.groot-core-db.tsv new file mode 100644 index 0000000..84ba023 --- /dev/null +++ b/outputs/raw/groot.groot-core-db.tsv @@ -0,0 +1,7 @@ +0 1 2 3 ARO confers_resistance_to resistance_to_drug_classes +groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221315 1221 0 156M7D1057M1D +groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 203 1920 2D1900M18D ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__tet(0/32/0)_4_AINH01000038 767 1920 1783M5D132M ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/outputs/raw/groot.groot-db.tsv b/outputs/raw/groot.groot-db.tsv new file mode 100644 index 0000000..aeca60b --- /dev/null +++ b/outputs/raw/groot.groot-db.tsv @@ -0,0 +1,45 @@ +0 1 2 3 ARO confers_resistance_to resistance_to_drug_classes +groot-db_RESFINDER__cfxA2_1_AF504914 321 966 286M1D328M1D344M6D ARO:3003002 ARO:0000044 ARO:3000007 +groot-db_RESFINDER__tet(40)_1_FJ158002 411 1221 1221M ARO:3000567 ARO:0000051 ARO:3000050 +groot-db_ARGANNOT__(Bla)cfxA5:AY769934:28-993:966 449 966 775M1D184M6D ARO:3003096 ARO:0000044 ARO:3000007 +groot-db_RESFINDER__erm(B)_12_U18931 238 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__erm(B)_7_AF368302 201 711 4D705M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__cfxA3_1_AF472622 519 966 960M6D ARO:3003003 ARO:0000044 ARO:3000007 +groot-db_ARGANNOT__(MLS)ErmB:M11180:714-1451:738 178 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__erm(B)_1_JN899585 214 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_ARGANNOT__(Bla)cfxA4:AY769933:1-966:966 450 966 960M6D ARO:3003005 ARO:0000044 ARO:3000007 +groot-db_CARD__gb|JQ740052|+|2108-3329|ARO:3000567|tet(40) 323 1222 530M2D690M ARO:3000567 ARO:0000051 ARO:3000050 +groot-db_ARGANNOT__(Tet)TetW:AJ222769:3687-5606:1920 204 1920 2D1900M15D3M ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_CARD__gb|AF472622|+|52-1018|ARO:3003003|CfxA3 519 967 960M7D ARO:3003003 ARO:0000044 ARO:3000007 +groot-db_RESFINDER__tet(W)_1_DQ060146 202 1920 2D1032M20D848M15D3M ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_CARD__gb|EU434751|+|658-2578|ARO:3000194|tetW 196 1920 2D1900M15D3M +groot-db_RESFINDER__tet(O/W)_1_AM889118 271 1889 968M13D104M10D773M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_RESFINDER__tet(W)_3_AJ427421 200 1920 2D1705M29D166M15D3M ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_RESFINDER__tet(Q)_1_L33696 1021 1926 1684M1D237M4D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_ARGANNOT__(MLS)ErmF:M14730:241-1041:801 321 801 598M10D189M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_ARGANNOT__(AGly)Aph7:GG774704:686456-687373:918254 918 0 912M6D +groot-db_RESFINDER__ant(6)-Ia_3_KF864551 217 867 852M15D ARO:3002629 ARO:0000040 ARO:0000016 +groot-db_ARGANNOT__(Bla)cfiA9:AB087234:1-750:750 79 750 15D732M3D ARO:3006921 ARO:0000020 ARO:3000007 +groot-db_RESFINDER__tet(O/W)_4_AM889121 289 1889 1242M22D604M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_RESFINDER__erm(F)_3_M17808 380 801 797M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__tet(O/W)_3_AM889120 264 1889 591M27D451M13D279M1D506M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_RESFINDER__erm(B)_9_AF299292 191 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_ARGANNOT__(Tet)Tet-32:DQ647324:181-2100:1920 148 1920 4D1897M19D ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_CARD__gb|AF118110|-|71-1037|ARO:3003002|CfxA2 452 967 963M4D ARO:3003002 ARO:0000044 ARO:3000007 +groot-db_RESFINDER__erm(B)_6_AF242872 192 747 4D304M6D418M15D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_ARGANNOT__(Bla)cfxA2:AF504910:1-966:966 338 966 101M1D401M2D455M6D ARO:3003002 ARO:0000044 ARO:3000007 +groot-db_ARGANNOT__(Tet)Tet-40:AM419751:14211-15431:1221317 1221 0 156M7D1058M +groot-db_CARD__gb|AF242872|+|2131-2878|ARO:3000375|ErmB 192 748 4D304M6D418M16D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__erm(B)_15_U48430 159 753 4D567M2D159M21D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +groot-db_RESFINDER__tet(W)_4_FN396364 216 1920 2D618M40D582M29D641M5D3M ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_RESFINDER__tet(Q)_4_Z21523 510 1926 1923M3D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_RESFINDER__tet(O/W)_2_AM889119 232 1889 560M14D175M13D323M10D507M6D144M1D115M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_RESFINDER__tet(O/W)_5_AM889122 269 1889 26D985M3D854M21D ARO:3007121 ARO:0000051 ARO:3000050 +groot-db_ARGANNOT__(Bla)OXA-347:JN086160:1583-2407:825 191 825 11D812M1D1M ARO:3001777 ARO:0000056 ARO:3000007 +groot-db_CARD__gb|AY769933|+|0-966|ARO:3003005|CfxA4 450 967 960M7D ARO:3003005 ARO:0000044 ARO:3000007 +groot-db_CARD__gb|JN086160|-|1582-2407|ARO:3001777|OXA-347 191 826 2D813M11D ARO:3001777 ARO:0000056 ARO:3000007 +groot-db_CARD__gb|AY769934|+|27-993|ARO:3003096|CfxA5 449 967 775M1D184M7D ARO:3003096 ARO:0000044 ARO:3000007 +groot-db_RESFINDER__tet(O)_4_AIOQ01000025 767 1920 1783M5D132M ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_RESFINDER__tet(0/32/0)_7_FP929050 718 1920 892M52D976M ARO:3000190 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +groot-db_ARGANNOT__(Tet)TetQ:Z21523:362-2287:1926 539 1974 1D1970M3D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/outputs/raw/groot.resfinder.tsv b/outputs/raw/groot.resfinder.tsv new file mode 100644 index 0000000..101dbcd --- /dev/null +++ b/outputs/raw/groot.resfinder.tsv @@ -0,0 +1,29 @@ +0 1 2 3 ARO confers_resistance_to resistance_to_drug_classes +cfiA9_1_AB087234 79 750 15D732M3D ARO:3006921 ARO:0000020 ARO:3000007 +erm(B)_11_M19270 132 738 4D211M7D278M6D230M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +ant(6)-Ia_3_KF864551 217 867 852M15D ARO:3002629 ARO:0000040 ARO:0000016 +tet(40)_3_AM419751 315 1221 156M7D1057M1D +erm(B)_15_U48430 159 753 4D567M2D159M21D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +blaOXA-347_1_JN086160 191 825 11D812M1D1M ARO:3001777 ARO:0000056 ARO:3000007 +erm(B)_9_AF299292 191 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(W)_1_DQ060146 201 1920 2D1032M20D848M18D ARO:3000194 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +cfxA2_1_AF504914 321 966 286M1D328M1D344M6D ARO:3003002 ARO:0000044 ARO:3000007 +tet(W)_5_AJ427421 199 1920 2D1705M29D166M18D +erm(B)_6_AF242872 192 747 4D304M6D418M15D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(40)_1_FJ158002 322 1221 1220M1D ARO:3000567 ARO:0000051 ARO:3000050 +erm(B)_1_JN899585 214 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(32)_2_EF626943 148 1920 4D1897M19D ARO:3000196 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +cfxA3_1_AF472622 519 966 960M6D ARO:3003003 ARO:0000044 ARO:3000007 +tet(Q)_4_Z21523 539 1974 1D1970M3D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 +tet(W)_6_FN396364 215 1920 2D618M40D582M29D641M8D +cfxA5_1_AY769934 449 966 775M1D184M6D ARO:3003096 ARO:0000044 ARO:3000007 +erm(B)_7_AF368302 201 711 4D705M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +erm(B)_10_U86375 178 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +cfxA4_1_AY769933 450 966 960M6D ARO:3003005 ARO:0000044 ARO:3000007 +tetO_4_AIOQ01000025 767 1920 1783M5D132M +erm(B)_12_U18931 238 738 4D732M2D ARO:3000375 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(W)_4_AJ427422 203 1920 2D1900M18D +erm(F)_2_M17124 321 801 598M10D189M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(40)_2_FJ158002 409 1221 1220M1D +erm(F)_3_M17808 380 801 797M4D ARO:3000498 ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867 ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026 +tet(Q)_1_L33696 1021 1926 1684M1D237M4D ARO:3000191 ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668 ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050 diff --git a/tests/test_lib.py b/tests/test_lib.py index 8422523..3690f8c 100644 --- a/tests/test_lib.py +++ b/tests/test_lib.py @@ -10,7 +10,10 @@ def test_map_to_aro(): ["gb|AAG57600.1|ARO:3000318|mphB", "sarg"], ["(Phe)cpt_strepv:U09991:AAB36569:1412-1948:537", "argannot"], ["MEG_4060|Metals|Multi-metal_resistance|Multi-metal_resistance_protein|MREA", "megares"], - ["gi:447201629:ref:WP_001278885.1:|FEATURES|cob(I)alamin_adenolsyltransferase|unclassified|cob(I)alamin_adenolsyltransferase", "deeparg"] + ["gi:447201629:ref:WP_001278885.1:|FEATURES|cob(I)alamin_adenolsyltransferase|unclassified|cob(I)alamin_adenolsyltransferase", "deeparg"], + ["argannot~~~(Bla)cfxA4~~~AY769933:1-966", 'groot', 'groot-argannot'], + ["ErmF.3000498.M17124.1181-1982.593", 'groot', 'groot-card'], + ["groot-db_RESFINDER__tet(W)_1_DQ060146", 'groot', 'groot-db'] ] ARO = lib.get_aro_ontology() @@ -21,13 +24,19 @@ def test_map_to_aro(): ARO.get_term('ARO:3000318'), ARO.get_term('ARO:3000249'), None, - ARO.get_term('ARO:0010004') + ARO.get_term('ARO:0010004'), + ARO.get_term('ARO:3003005'), + ARO.get_term('ARO:3000498'), + ARO.get_term('ARO:3000194') ] for t, e in zip(test_cases, expected_output): - assert map_to_aro(t[0], t[1]) == e + if t[1] == 'groot': + assert map_to_aro(t[0], t[1], t[2]) == e + else: + assert map_to_aro(t[0], t[1]) == e -@pytest.mark.parametrize('database', ['argannot', 'megares', 'ncbi', 'resfinder', 'resfinderfg']) +@pytest.mark.parametrize('database', ['argannot', 'megares', 'ncbi', 'resfinder', 'resfinderfg', 'groot']) def test_get_aro_mapping_table_smoke(database): df = get_aro_mapping_table(database) assert len(df) > 0 diff --git a/tests/test_normalizers.py b/tests/test_normalizers.py index 31026cb..f3ed5ea 100644 --- a/tests/test_normalizers.py +++ b/tests/test_normalizers.py @@ -85,4 +85,29 @@ def test_amrfinderplus_normalizer(hamronized): normed = get_normed(normalizer, input_file) golden_file = pd.read_csv(os.path.join('./outputs/', folder, f'amrfinderplus.ncbi.orfs.tsv'), sep='\t') - pd.testing.assert_frame_equal(normed, golden_file) \ No newline at end of file + pd.testing.assert_frame_equal(normed, golden_file) + +@pytest.mark.parametrize('database', ['argannot', 'resfinder', 'card', 'groot-db', 'groot-core-db']) +def test_groot_normalizer_raw(database): + if 'groot' not in database: + normalizer = argnorm.GrootNormalizer(database=f'groot-{database}', is_hamronized=False) + else: + normalizer = argnorm.GrootNormalizer(database=f'groot-db', is_hamronized=False) + + input_path = f'./examples/raw/groot.{database}.tsv' + normed = get_normed(normalizer, input_path) + normed.columns = normed.columns.astype(str) + golden_file = pd.read_csv(os.path.join('./outputs/', 'raw', f'groot.{database}.tsv'), sep='\t') + pd.testing.assert_frame_equal(normed, golden_file) + +@pytest.mark.parametrize('database', ['argannot', 'resfinder', 'card', 'groot-db', 'groot-core-db']) +def test_groot_normalizer_raw(database): + if 'groot' not in database: + normalizer = argnorm.GrootNormalizer(database=f'groot-{database}', is_hamronized=True) + else: + normalizer = argnorm.GrootNormalizer(database=f'groot-db', is_hamronized=True) + input_path = f'./examples/hamronized/groot.{database}.tsv' + normed = get_normed(normalizer, input_path) + normed.columns = normed.columns.astype(str) + golden_file = pd.read_csv(os.path.join('./outputs/', 'hamronized', f'groot.{database}.tsv'), sep='\t') + pd.testing.assert_frame_equal(normed, golden_file)