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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Oct 2, 2024
1 parent 819ae2e commit 66ca539
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Showing 11 changed files with 14,330 additions and 14,530 deletions.
10,506 changes: 5,253 additions & 5,253 deletions data/alleles.tsv
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2 changes: 0 additions & 2 deletions data/chromosome1.contig
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Expand Up @@ -33317,8 +33317,6 @@ FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20100827"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20100827"
FT /controlled_curation="term=species distribution, conserved
FT in fungi only; date=20100827"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20100827"
FT /primary_name="aim18"
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25 changes: 8 additions & 17 deletions data/chromosome2.contig
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Expand Up @@ -9439,8 +9439,6 @@ FT /colour=7
FT /product="ribosome biogenesis protein Rrp14 (predicted)"
FT /db_xref="SPD:08/08C03"
FT /systematic_id="SPBC947.07"
FT /controlled_curation="term=surfeit locus (SURF40 family);
FT date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -22532,8 +22530,6 @@ FT /primary_name="shy1"
FT /product="cytochrome c oxidase assembly protein Shy1"
FT /db_xref="SPD:13/13E04"
FT /systematic_id="SPBC1215.01"
FT /controlled_curation="term=surfeit locus (SURF40 family);
FT date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -34603,8 +34599,8 @@ FT CDS complement(2289372..2290058)
FT /EC_number="1.10.2.2"
FT /colour=2
FT /primary_name="rip1"
FT /product="Rieske iron-sulfur protein,
FT ubiquinol-cytochrome-c reductase complex subunit 5, Rip1"
FT /product="ubiquinol-cytochrome-c reductase complex subunit
FT 5, Rieske iron-sulfur protein, Rip1"
FT /db_xref="SPD:31/31G11"
FT /systematic_id="SPBC16H5.06"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -36943,18 +36939,12 @@ FT 3'UTR complement(2432036..2433109)
FT /systematic_id="SPBC21D10.07"
FT /db_xref="PMID:21511999"
FT CDS join(2432142..2432227,2432278..2433025)
FT /colour=10
FT /product="conserved fungal protein"
FT /colour=12
FT /product="Schizosaccharomyces specific protein"
FT /db_xref="SPD:43/43E05"
FT /systematic_id="SPBC21D10.08c"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20140815"
FT /controlled_curation="term=species distribution, conserved
FT in fungi only; date=20140815"
FT /controlled_curation="term=species distribution, no
FT apparent S. cerevisiae ortholog; date=20140815"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20140815"
FT /controlled_curation="term=species distribution,
FT Schizosaccharomyces specific; date=20240929"
FT 3'UTR 2433026..2433891
FT /systematic_id="SPBC21D10.08c"
FT /db_xref="PMID:21511999"
Expand Down Expand Up @@ -44080,7 +44070,8 @@ FT /systematic_id="SPNCRNA.5873"
FT /product="non-coding RNA"
FT CDS complement(2898280..2899206)
FT /colour=12
FT /product="Schizosaccharomyces specific protein"
FT /product="Schizosaccharomyces specific protein, possibly
FT isoprenylated"
FT /db_xref="SPD:12/12H11"
FT /systematic_id="SPBP4H10.14c"
FT /controlled_curation="term=species distribution,
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10 changes: 6 additions & 4 deletions data/chromosome3.contig
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Expand Up @@ -6873,8 +6873,6 @@ FT /colour=7
FT /product="COPII adaptor Erv29 (predicted)"
FT /db_xref="SPD:12/12E12"
FT /systematic_id="SPCC970.06"
FT /controlled_curation="term=surfeit locus (SURF40 family);
FT date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -23282,8 +23280,9 @@ FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.7466"
FT /product="non-coding RNA"
FT CDS complement(join(1691782..1692727,1692827..1693416,1693516..1693936,1694086..1694432))
FT /colour=7
FT /product="DNA-binding transcription factor (predicted)"
FT /colour=2
FT /product="DNA-binding transcription factor, sulfur
FT depletion response, Sdr1"
FT /db_xref="SPD:38/38G10"
FT /systematic_id="SPCC417.09c"
FT /controlled_curation="term=zinc finger protein;
Expand All @@ -23298,6 +23297,9 @@ FT /controlled_curation="term=species distribution, conserved
FT in fungi only; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20080202"
FT /controlled_curation="term=name description, sulfur
FT depletion response; db_xref=PMID:39105351; date=20241001"
FT /primary_name="sdr1"
FT lncRNA 1692870..1693836
FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.7467"
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18 changes: 9 additions & 9 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-9 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-13 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
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-20 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-24 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-2 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-87 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-47 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-45 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-2 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-10 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
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-114 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-8 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-16 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-14 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
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