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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Dec 11, 2024
1 parent 336be4e commit f3dc073
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Showing 10 changed files with 13,395 additions and 13,396 deletions.
10,450 changes: 5,225 additions & 5,225 deletions data/alleles.tsv
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15 changes: 9 additions & 6 deletions data/chromosome1.contig
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Expand Up @@ -6348,7 +6348,7 @@ FT score=63.430200; db_xref=PMID:30566651"
FT CDS 468720..469826
FT /colour=7
FT /product="phospho-2-dehydro-3-deoxyheptonate aldolase
FT (predicted)"
FT Aro4"
FT /systematic_id="SPAC24H6.10c"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20100820"
Expand All @@ -6357,6 +6357,8 @@ FT in eukaryotes; date=20100820"
FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20100820"
FT /db_xref="SPD:17/17D05"
FT /primary_name="aro4"
FT /synomym="aro3"
FT 3'UTR 469827..469890
FT /db_xref="EMBL:AU007393"
FT /systematic_id="SPAC24H6.10c"
Expand Down Expand Up @@ -36577,9 +36579,7 @@ FT /systematic_id="SPAC6B12.18"
FT /db_xref="PMID:21511999"
FT CDS complement(2416782..2418047)
FT /colour=7
FT /product="2-aminoadipate
FT transaminase/kynurenine-oxoglutarate transaminase
FT (predicted)"
FT /product="2-aminoadipate transaminase (predicted)"
FT /systematic_id="SPAC6B12.04c"
FT /db_xref="SPD:20/20C04"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -72037,7 +72037,8 @@ FT /systematic_id="SPAC1782.02c"
FT /db_xref="PMID:21511999"
FT CDS complement(join(4760301..4760651,4760752..4760886))
FT /colour=10
FT /product="conserved fungal protein"
FT /product="conserved fungal protein, possible MARVEL
FT domain, implicated in membrane organization"
FT /systematic_id="SPAC1782.02c"
FT /db_xref="SPD:06/06D03"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -80834,14 +80835,16 @@ FT /db_xref="PMID:21511999"
FT CDS complement(join(5326720..5327829,5328101..5328109))
FT /colour=7
FT /product="phospho-2-dehydro-3-deoxyheptonate aldolase
FT (predicted)"
FT Aro3"
FT /systematic_id="SPAP8A3.07c"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20100820"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20100820"
FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20100820"
FT /primary_name="aro3"
FT /synontm="aro4"
FT lncRNA 5326840..5328155
FT /db_xref="PMID:29914874"
FT /db_xref="PMID:21511999"
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10 changes: 3 additions & 7 deletions data/chromosome2.contig
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Expand Up @@ -67072,17 +67072,13 @@ FT 3'UTR 4376811..4377177
FT /systematic_id="SPBC1539.08"
FT /db_xref="PMID:21511999"
FT CDS complement(4377221..4379500)
FT /EC_number="4.1.3.27"
FT /EC_number="4.1.1.48"
FT /EC_number="5.3.1.24"
FT /colour=2
FT /primary_name="trp1"
FT /product="anthranilate synthase component II,
FT multifunctional enzyme Trp1"
FT /product="phosphoribosylanthranilate
FT isomerase/indole-3-glycerol-phosphate synthase/unknown
FT aminotransferase, multifunctional enzyme Trp1"
FT /db_xref="SPD:33/33G02"
FT /systematic_id="SPBC1539.09c"
FT /controlled_curation="term=catalytic activity,
FT multifunctional enzyme; cv=cat_act; date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20100820"
FT /controlled_curation="term=species distribution, conserved
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Binary file modified data/genome.pickle
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20 changes: 10 additions & 10 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-8 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-26 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-19 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-86 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-18 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-17 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
SPAC140.02 SPAC140.02:allele-3 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-14 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-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-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
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-38 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-52 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-25 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-24 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 D47DN,D47N 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 D58N,D58DN 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 D79DN,D79N multi_shift_fix D366|D366 2 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
Expand All @@ -18,4 +18,4 @@ 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 D286DN,D286N 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 D356DN,D356N multi_shift_fix D366|D366 7 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
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-9 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
SPNCRNA.1712 SPNCRNA.1712:allele-12 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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