From d79b89040a5c6a8944e903e958663c95a74849d0 Mon Sep 17 00:00:00 2001 From: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Date: Wed, 7 Aug 2024 08:25:13 +0530 Subject: [PATCH] ADD our own raw & hamronized example groot outputs to test groot normalizer (#61) --- examples/hamronized/groot.argannot.tsv | 13 ++++++ examples/hamronized/groot.card.tsv | 27 +++++++++++++ examples/hamronized/groot.groot-core-db.tsv | 7 ++++ examples/hamronized/groot.groot-db.tsv | 45 +++++++++++++++++++++ examples/hamronized/groot.resfinder.tsv | 29 +++++++++++++ examples/raw/groot.argannot.tsv | 12 ++++++ examples/raw/groot.card.tsv | 26 ++++++++++++ examples/raw/groot.groot-core-db.tsv | 6 +++ examples/raw/groot.groot-db.tsv | 44 ++++++++++++++++++++ examples/raw/groot.resfinder.tsv | 28 +++++++++++++ examples/scripts/get_groot_examples.py | 25 ++++++++++++ 11 files changed, 262 insertions(+) create mode 100644 examples/hamronized/groot.argannot.tsv create mode 100644 examples/hamronized/groot.card.tsv create mode 100644 examples/hamronized/groot.groot-core-db.tsv create mode 100644 examples/hamronized/groot.groot-db.tsv create mode 100644 examples/hamronized/groot.resfinder.tsv create mode 100644 examples/raw/groot.argannot.tsv create mode 100644 examples/raw/groot.card.tsv create mode 100644 examples/raw/groot.groot-core-db.tsv create mode 100644 examples/raw/groot.groot-db.tsv create mode 100644 examples/raw/groot.resfinder.tsv create mode 100644 examples/scripts/get_groot_examples.py diff --git a/examples/hamronized/groot.argannot.tsv b/examples/hamronized/groot.argannot.tsv new file mode 100644 index 0000000..0862378 --- /dev/null +++ b/examples/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 +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 diff --git a/examples/hamronized/groot.card.tsv b/examples/hamronized/groot.card.tsv new file mode 100644 index 0000000..258da1e --- /dev/null +++ b/examples/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 +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 diff --git a/examples/hamronized/groot.groot-core-db.tsv b/examples/hamronized/groot.groot-core-db.tsv new file mode 100644 index 0000000..e935333 --- /dev/null +++ b/examples/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 +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 diff --git a/examples/hamronized/groot.groot-db.tsv b/examples/hamronized/groot.groot-db.tsv new file mode 100644 index 0000000..b17e8e8 --- /dev/null +++ b/examples/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 +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 diff --git a/examples/hamronized/groot.resfinder.tsv b/examples/hamronized/groot.resfinder.tsv new file mode 100644 index 0000000..233c765 --- /dev/null +++ b/examples/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 +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 diff --git a/examples/raw/groot.argannot.tsv b/examples/raw/groot.argannot.tsv new file mode 100644 index 0000000..c884c1f --- /dev/null +++ b/examples/raw/groot.argannot.tsv @@ -0,0 +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 diff --git a/examples/raw/groot.card.tsv b/examples/raw/groot.card.tsv new file mode 100644 index 0000000..acf02c1 --- /dev/null +++ b/examples/raw/groot.card.tsv @@ -0,0 +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 diff --git a/examples/raw/groot.groot-core-db.tsv b/examples/raw/groot.groot-core-db.tsv new file mode 100644 index 0000000..67b2eb1 --- /dev/null +++ b/examples/raw/groot.groot-core-db.tsv @@ -0,0 +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 diff --git a/examples/raw/groot.groot-db.tsv b/examples/raw/groot.groot-db.tsv new file mode 100644 index 0000000..4e7224d --- /dev/null +++ b/examples/raw/groot.groot-db.tsv @@ -0,0 +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 diff --git a/examples/raw/groot.resfinder.tsv b/examples/raw/groot.resfinder.tsv new file mode 100644 index 0000000..6c9fa0a --- /dev/null +++ b/examples/raw/groot.resfinder.tsv @@ -0,0 +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 diff --git a/examples/scripts/get_groot_examples.py b/examples/scripts/get_groot_examples.py new file mode 100644 index 0000000..f235f51 --- /dev/null +++ b/examples/scripts/get_groot_examples.py @@ -0,0 +1,25 @@ +import subprocess + +# Following this documentation: https://groot-documentation.readthedocs.io/en/latest/using-groot.html#an-example + +def get_input_data(): + subprocess.run(""" + echo Getting sample fastq file + fastq-dump SRR4454613 + """, shell=True) + +def get_groot_example(db, fastq): + command = f""" + echo generating GROOT {db} db example + mkdir {db} && cd {db} + groot get -d {db} + groot index -m {db}.90 -i grootIndex -w 100 -p 8 + groot align -i grootIndex -f {fastq} -p 8 | groot report -c 0.95 + cd .. && rm -rf {db} + """ + + subprocess.check_call(command, shell=True) + +get_input_data() +for db in ['resfinder', 'arg-annot', 'groot-db', 'groot-core-db', 'card']: + get_groot_example(db, '../SRR4454613.fastq') \ No newline at end of file