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address #66 (comment)
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@manulera
manulera committed Aug 16, 2023
1 parent cda2b07 commit 3ef4c14
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Showing 10 changed files with 15,583 additions and 16,086 deletions.
17,943 changes: 8,823 additions & 9,120 deletions data/alleles.tsv
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5,134 changes: 2,567 additions & 2,567 deletions data/pombase-chado.modifications
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38 changes: 38 additions & 0 deletions filter_alleles_pombase.py
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"""
Filters out the alleles without phenotype annotations based on the canto allele list.
Just to make sure that there is no allele in canto that has no annotations, but has an annotation in a phaf file,
we also use the phaf files.
It overwrites the 1st argument alleles.tsv file.
usage: python alleles.tsv alleles_canto.tsv alleles_phaf.tsv
"""

import pandas
import sys


def main(alleles_file, canto_alleles_file, phaf_alleles_file):
alleles = pandas.read_csv(alleles_file, sep='\t', na_filter=False)

canto_alleles = pandas.read_csv(canto_alleles_file, sep='\t', na_filter=False)
canto_alleles.rename(columns={'gene_systematic_id': 'systematic_id'}, inplace=True)

phaf_alleles = pandas.read_csv(phaf_alleles_file, sep='\t', na_filter=False)
phaf_alleles.columns = ['systematic_id', 'allele_description', 'gene_name', 'allele_name', 'allele_synonym', 'allele_type', 'reference']

for df in (alleles, canto_alleles, phaf_alleles):
df['unique_id'] = df['systematic_id'] + '$' + df['allele_name'] + '$' + df['allele_description']

alleles_without_annotations = canto_alleles[(canto_alleles['annotation_count'] == 0) & ~canto_alleles['unique_id'].isin(set(phaf_alleles['unique_id']))]

alleles = alleles[~alleles['unique_id'].isin(set(alleles_without_annotations['unique_id']))]
alleles.to_csv(alleles_file, sep='\t', index=False)


if __name__ == '__main__':

if len(sys.argv) != 4:
print(__doc__)
sys.exit(1)

main(sys.argv[1], sys.argv[2], sys.argv[3])
9 changes: 8 additions & 1 deletion get_data.sh
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Expand Up @@ -13,7 +13,14 @@ curl -k https://curation.pombase.org/dumps/latest_build/exports/all-allele-detai
# Replace the first line by the right column names
echo -ne 'systematic_id\tgene_name\tallele_id\tallele_name\tallele_description\tallele_type\treference\n' > data/alleles.tsv
tail -n +2 data/alleles_raw.tsv|sort|uniq|grep -v $'\t'deletion|grep -v wild_type >> data/alleles.tsv
rm data/alleles_raw.tsv

# Download phaf and canto alleles to filter out the ones without annotations
curl -k https://curation.pombase.org/data/pombe-allele-table.tsv --output data/alleles_canto.tsv
curl -k https://www.pombase.org/data/annotations/Phenotype_annotations/phenotype_annotations.pombase.phaf.gz --output data/phenotype_annotations.phaf.gz
gzip -fd data/phenotype_annotations.phaf.gz
cut -f 2,4,9,10,11,12,18 data/phenotype_annotations.phaf|sort|uniq|grep -v $'\t'deletion|grep -v wild_type > data/alleles_phaf.tsv
python filter_alleles_pombase.py data/alleles.tsv data/alleles_canto.tsv data/alleles_phaf.tsv
rm data/alleles_raw.tsv data/alleles_canto.tsv data/alleles_phaf.tsv

echo -e "${GREEN}Getting contig files${NC}"
# Get genome sequence with annotations
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47 changes: 9 additions & 38 deletions results/allele_auto_fix.tsv
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systematic_id allele_id allele_name allele_description allele_type change_description_to change_name_to change_type_to auto_fix_comment sequence_error solution_index allele_parts rules_applied reference
SPAC10F6.09c SPAC10F6.09c:allele-38 psm3-QQ K105Q K106Q amino_acid_mutation K105Q,K106Q syntax_error K105Q|K106Q amino_acid_mutation:single_aa|amino_acid_mutation:single_aa PMID:33176147
SPAC11H11.01 SPAC11H11.01:allele-2 sst6-Q207STOP Q207->stop nonsense_mutation Q207* partial_amino_acid_deletion syntax_and_type_error Q207->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC1296.01c SPAC1296.01c:allele-2 SPAC1296.01c-Q175STOP Q175->stop nonsense_mutation Q175* partial_amino_acid_deletion syntax_and_type_error Q175->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC13C5.03 SPAC13C5.03:allele-6 tht1-D543* D543->stop nonsense_mutation D543* partial_amino_acid_deletion syntax_and_type_error D543->stop nonsense_mutation:stop_codon_text PMID:9442101
SPAC140.02 SPAC140.02:allele-8 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC1565.08 SPAC1565.08:allele-11 cdc48-A439T A439T amino_acid_mutation A433T cdc48-A433T old_coords_fix, revision 8148: join(1306439..1306512,1306569..1308942) A439 A439T amino_acid_mutation:single_aa PMID:28552615
SPAC17G6.05c SPAC17G6.05c:allele-2 bro1-E644STOP E644->stop nonsense_mutation E644* partial_amino_acid_deletion syntax_and_type_error E644->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC140.02 SPAC140.02:allele-9 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-15 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPAC19A8.05c SPAC19A8.05c:allele-7 sst4-Q202STOP Q202->stop nonsense_mutation Q202* partial_amino_acid_deletion syntax_and_type_error Q202->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC19A8.05c SPAC19A8.05c:allele-6 sst4-W170STOP W170->stop nonsense_mutation W170* partial_amino_acid_deletion syntax_and_type_error W170->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC22F3.13 SPAC22F3.13:allele-3 tsc1-Q688STOP Q688STOP nonsense_mutation Q688* partial_amino_acid_deletion syntax_and_type_error Q688STOP nonsense_mutation:stop_codon_text PMID:34028542
SPAC25G10.04c SPAC25G10.04c:allele-5 rec10-133 Q729->stop amino_acid_mutation Q729* partial_amino_acid_deletion syntax_and_type_error Q729->stop nonsense_mutation:stop_codon_text PMID:28469148
SPAC3H1.10 SPAC3H1.10:allele-12 pcs2-N147D N147D nonsense_mutation amino_acid_mutation type_error N147D amino_acid_mutation:single_aa PMID:34028542
SPAC4G8.05 SPAC4G8.05:allele-2 ppk14-R148STOP R148->stop nonsense_mutation R148* partial_amino_acid_deletion syntax_and_type_error R148->stop nonsense_mutation:stop_codon_text PMID:34028542
SPAC57A10.14 SPAC57A10.14:allele-3 sgf11-Q64->stop Q64->stop nonsense_mutation Q64* partial_amino_acid_deletion syntax_and_type_error Q64->stop nonsense_mutation:stop_codon_text PMID:29352077
SPAC630.03 SPAC630.03:allele-8 arp3-L155C L155C amino_acid_insertion amino_acid_mutation type_error L155C amino_acid_mutation:single_aa PMID:21676862
SPAC630.13c SPAC630.13c:allele-4 tsc2-L636STOP L636STOP nonsense_mutation L636* partial_amino_acid_deletion syntax_and_type_error L636STOP nonsense_mutation:stop_codon_text PMID:34028542
SPAC8C9.03 SPAC8C9.03:allele-5 cgs1-180 L86->stop amino_acid_mutation L86* partial_amino_acid_deletion syntax_and_type_error L86->stop nonsense_mutation:stop_codon_text PMID:15189983
SPAC977.10 SPAC977.10:allele-119 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
SPBC215.05 SPBC215.05:allele-3 gpd1-G4BS TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
SPBC28F2.12 SPBC28F2.12:allele-16 rpb1-CTD-P3A(r2-r29-2) CTD-P3A(r2-r29-2) amino_acid_insertion_and_mutation amino_acid_mutation type_error CTD-P3A(r2-r29-2) amino_acid_mutation:CTD PMID:32282918,PMID:33579781,PMID:34389684
SPBC28F2.12 SPBC28F2.12:allele-14 rpb1-CTD-S2A(r1-r12)delta(r13-r29) CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation CTD-S2A(r1-r12),delta(r13-r29) syntax_error CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation:CTD PMID:22144909
SPBC28F2.12 SPBC28F2.12:allele-7 rpb1-CTD-S2A(r5-r29)S7A(r5-r29) CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation CTD-S2A(r5-r29),S7A(r5-r29) syntax_error CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation:CTD PMID:22771993
SPBC32C12.02 SPBC32C12.02:allele-18 ste11-promoter mutant -194--229 partial_nucleotide_deletion (-229)-(-194) syntax_error -194--229 partial_nucleotide_deletion:usual PMID:10982411
SPBC3H7.13 SPBC3H7.13:allele-2 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-17 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPBC4B4.06 SPBC4B4.06:allele-2 vps25-W113STOP W113->stop nonsense_mutation W113* partial_amino_acid_deletion syntax_and_type_error W113->stop nonsense_mutation:stop_codon_text PMID:34028542
SPBC8D2.03c SPBC8D2.03c:allele-7 hhf2-K12R K12R amino_acid_mutation K13R histone_fix K12 K12R amino_acid_mutation:single_aa PMID:30992049
SPBC8D2.03c SPBC8D2.03c:allele-8 hhf2-K16R K16R amino_acid_mutation K17R histone_fix K16 K16R amino_acid_mutation:single_aa PMID:30992049
SPBC8D2.03c SPBC8D2.03c:allele-5 hhf2-K5R K5R amino_acid_mutation K6R histone_fix K5 K5R amino_acid_mutation:single_aa PMID:30992049
SPBC8D2.03c SPBC8D2.03c:allele-6 hhf2-K8R K8R amino_acid_mutation K9R histone_fix K8 K8R amino_acid_mutation:single_aa PMID:30992049
SPBP35G2.14 SPBP35G2.14:allele-5 puf2-Q40STOP Q40->stop nonsense_mutation Q40* partial_amino_acid_deletion syntax_and_type_error Q40->stop nonsense_mutation:stop_codon_text PMID:34028542
SPBP35G2.14 SPBP35G2.14:allele-6 puf2-Y416STOP Y416->stop nonsense_mutation Y416* partial_amino_acid_deletion syntax_and_type_error Y416->stop nonsense_mutation:stop_codon_text PMID:34028542
SPCC18B5.03 SPCC18B5.03:allele-14 wee1::ura4+ disruption wee1::ura4 syntax_error wee1::ura4+ disruption:usual PMID:7957098
SPCC23B6.01c SPCC23B6.01c:allele-2 osh6-S117STOP S117->stop nonsense_mutation S117* partial_amino_acid_deletion syntax_and_type_error S117->stop nonsense_mutation:stop_codon_text PMID:34028542
SPCC338.08 SPCC338.08:allele-63 slr9-1 R162->stop nonsense_mutation R162* partial_amino_acid_deletion syntax_and_type_error R162->stop nonsense_mutation:stop_codon_text PMID:18378696
SPCC4G3.15c SPCC4G3.15c:allele-2 not2-E31STOP E31->stop nonsense_mutation E31* partial_amino_acid_deletion syntax_and_type_error E31->stop nonsense_mutation:stop_codon_text PMID:34028542
SPCC584.15c SPCC584.15c:allele-2 aly3-R457STOP R457->stop amino_acid_mutation R457* partial_amino_acid_deletion syntax_and_type_error R457->stop nonsense_mutation:stop_codon_text PMID:34028542
SPCC645.07 SPCC645.07:allele-12 rgf1-Nes2* L1149A,I1151* amino_acid_mutation amino_acid_deletion_and_mutation type_error L1149A|I1151* amino_acid_mutation:single_aa|nonsense_mutation:stop_codon_star PMID:24478458
SPAC977.10 SPAC977.10:allele-94 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
SPBC215.05 SPBC215.05:allele-2 gpd1-G4BS TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
SPBC28F2.12 SPBC28F2.12:allele-12 rpb1-CTD-P3A(r2-r29-2) CTD-P3A(r2-r29-2) amino_acid_insertion_and_mutation amino_acid_mutation type_error CTD-P3A(r2-r29-2) amino_acid_mutation:CTD PMID:32282918,PMID:33579781,PMID:34389684
SPBC28F2.12 SPBC28F2.12:allele-20 rpb1-CTD-S2A(r1-r12)delta(r13-r29) CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation CTD-S2A(r1-r12),delta(r13-r29) syntax_error CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation:CTD PMID:22144909
SPBC28F2.12 SPBC28F2.12:allele-5 rpb1-CTD-S2A(r5-r29)S7A(r5-r29) CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation CTD-S2A(r5-r29),S7A(r5-r29) syntax_error CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation:CTD PMID:22771993
SPBC3H7.13 SPBC3H7.13:allele-3 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-7 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPCC18B5.03 SPCC18B5.03:allele-20 wee1::ura4+ disruption wee1::ura4 syntax_error wee1::ura4+ disruption:usual PMID:7957098
SPCC757.07c SPCC757.07c:allele-3 ctt1-G4BS ATGACGT(-428)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error ATGACGT(-428)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
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