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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Nov 17, 2024
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Showing 10 changed files with 12,384 additions and 12,378 deletions.
10,542 changes: 5,275 additions & 5,267 deletions data/alleles.tsv
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12 changes: 2 additions & 10 deletions data/chromosome1.contig
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Expand Up @@ -4185,9 +4185,6 @@ FT db_xref=PMID:22683269; date=20130715"
FT /controlled_curation="term=misc, deletion mutant
FT expression profiling; db_xref=PMID:18025105;
FT date=20090110"
FT /controlled_curation="term=pathway, Mad2-dependent
FT checkpoint response; cv=pathway; db_xref=PMID:16478992;
FT date=20060420"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -23146,8 +23143,6 @@ FT /controlled_curation="term=misc, promoter contains CRE
FT element; db_xref=PMID:20032302; date=20100624"
FT /controlled_curation="term=misc, promoter contains RLM1
FT element; db_xref=PMID:20032302; date=20100624"
FT /controlled_curation="term=pathway, Mkh1-Pek1-Spm1 MAP
FT kinase; db_xref=PMID:20032302; date=20100624"
FT 5'UTR complement(1571261..1571589)
FT /systematic_id="SPAC1705.03c"
FT /db_xref="PMID:30566651"
Expand Down Expand Up @@ -28565,8 +28560,6 @@ FT within the plasma membrane, faster at cell sides than at
FT cell tips, and the GDP-bound form diffuses faster than the
FT GTP-bound form; db_xref=PMID:25837586; date=20161206"
FT /controlled_curation="term=Rho family; date=19700101"
FT /controlled_curation="term=pathway, Ras1-Scd; cv=pathway;
FT date=20080718"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -45417,7 +45410,8 @@ FT /systematic_id="SPAPB1A11.04c"
FT /db_xref="PMID:21511999"
FT CDS 2984786..2986009
FT /colour=10
FT /product="FMN-dependent alpha-hydroxy acid dehydrogenase"
FT /product="FMN-dependent alpha-hydroxy acid dehydrogenase,
FT probable lactate dehydrogenase"
FT /systematic_id="SPAPB1A11.03"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20081110"
Expand Down Expand Up @@ -53503,8 +53497,6 @@ FT /controlled_curation="term=pleckstrin homology domain;
FT date=20061128"
FT /controlled_curation="term=calponin homology (CH) domain;
FT db_xref=Pfam:PF06395; date=20061128"
FT /controlled_curation="term=pathway, Ras1-Scd; cv=pathway;
FT date=19700101"
FT /controlled_curation="term=octicosapeptide repeat;
FT date=19700101"
FT /controlled_curation="term=species distribution, conserved
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5 changes: 3 additions & 2 deletions data/chromosome2.contig
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Expand Up @@ -26845,8 +26845,9 @@ FT /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT condition=FYECO:0000126; during=GO:0072690;
FT score=2.768810; db_xref=PMID:30566651"
FT CDS join(1786332..1786414,1786478..1787607,1787643..1787917)
FT /colour=10
FT /product="zf-CHY type zinc finger protein"
FT /colour=7
FT /product="zf-CHY type zinc finger protein involved in
FT rescue of stalled ribosomes"
FT /db_xref="SPD:23/23A06"
FT /systematic_id="SPBC18H10.09"
FT /controlled_curation="term=zf-CHY; date=19700101"
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Binary file modified data/genome.pickle
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16 changes: 8 additions & 8 deletions results/allele_auto_fix.tsv
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@@ -1,14 +1,14 @@
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
SPAC140.02 SPAC140.02:allele-4 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-10 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPAC23C4.19 SPAC23C4.19:allele-20 spt5-CTD-T1E(7) 801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS amino_acid_insertion_and_mutation amino_acid_insertion_and_deletion type_error 801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard PMID:32366382
SPAC56E4.04c SPAC56E4.04c:allele-5 cut6-1 L1910S amino_acid_mutation L1877S old_coords_fix, revision 8148: complement(join(1246095..1252807,1253430..1253559)) L1910 L1910S amino_acid_mutation:single_aa PMID:37792890
SPAC977.10 SPAC977.10:allele-56 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
SPAC23C4.19 SPAC23C4.19:allele-17 spt5-CTD-T1E(7) 801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS amino_acid_insertion_and_mutation amino_acid_insertion_and_deletion type_error 801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard PMID:32366382
SPAC56E4.04c SPAC56E4.04c:allele-8 cut6-1 L1910S amino_acid_mutation L1877S old_coords_fix, revision 8148: complement(join(1246095..1252807,1253430..1253559)) L1910 L1910S amino_acid_mutation:single_aa PMID:37792890
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-49 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-8 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
SPBC28F2.12 SPBC28F2.12:allele-13 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-15 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-7 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-8 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPBC428.08c SPBC428.08c:allele-12 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D47N,D47DN multi_shift_fix D366|D366 0 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D58DN,D58N multi_shift_fix D366|D366 1 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D79N,D79DN multi_shift_fix D366|D366 2 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
Expand All @@ -17,5 +17,5 @@ SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D282N,D282DN multi_shift_fix D366|D366 5 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D286N,D286DN multi_shift_fix D366|D366 6 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D356N,D356DN multi_shift_fix D366|D366 7 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC757.07c SPCC757.07c:allele-2 ctt1-G4BS ATGACGT(-428)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error ATGACGT(-428)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
SPNCRNA.1712 SPNCRNA.1712:allele-2 nc-pho1-dual-PAS-mut ATTTTT-342-CTCGAG,AATAAA-568-GGCGGG nucleotide_mutation ATTTTT342CTCGAG,AATAAA568GGCGGG syntax_error ATTTTT-342-CTCGAG|AATAAA-568-GGCGGG nucleotide_mutation:multiple_nt|nucleotide_mutation:multiple_nt PMID:30355770,PMID:36882296
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
SPNCRNA.1712 SPNCRNA.1712:allele-5 nc-pho1-dual-PAS-mut ATTTTT-342-CTCGAG,AATAAA-568-GGCGGG nucleotide_mutation ATTTTT342CTCGAG,AATAAA568GGCGGG syntax_error ATTTTT-342-CTCGAG|AATAAA-568-GGCGGG nucleotide_mutation:multiple_nt|nucleotide_mutation:multiple_nt PMID:30355770,PMID:36882296
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