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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Aug 21, 2024
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10,440 changes: 5,220 additions & 5,220 deletions data/alleles.tsv
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20 changes: 11 additions & 9 deletions data/chromosome1.contig
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Expand Up @@ -1701,8 +1701,8 @@ FT /systematic_id="SPAC11D3.18c"
FT /db_xref="PMID:21511999"
FT CDS complement(144862..146358)
FT /colour=7
FT /product="carboxylic acid transmembrane transporter
FT (predicted)"
FT /product="plasma membrane carboxylic acid transmembrane
FT transporter"
FT /systematic_id="SPAC11D3.18c"
FT /db_xref="SPD:24/24B10"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -6595,8 +6595,8 @@ FT /systematic_id="SPAC24H6.13"
FT /db_xref="PMID:21511999"
FT CDS complement(457061..459676)
FT /colour=7
FT /product="calcium ion transmembrane transporter
FT (predicted)"
FT /product="plasma membrane calcium permeable gated cation
FT channel"
FT /systematic_id="SPAC24H6.13"
FT /controlled_curation="term=orthologous to S. cerevisiae
FT YOL084W; date=19700101"
Expand Down Expand Up @@ -12333,8 +12333,7 @@ FT condition=FYECO:0000126; during=GO:0072690; score=7.12668;
FT db_xref=PMID:30566651"
FT CDS join(823739..823784,823894..826229)
FT /colour=7
FT /product="calcium ion transmembrane transporter
FT (predicted)"
FT /product="plasma calcium permeable gated cation channel"
FT /systematic_id="SPAC2G11.09"
FT /db_xref="SPD:28/28H07"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -28886,7 +28885,8 @@ FT /systematic_id="SPAC1002.16c"
FT /db_xref="PMID:21511999"
FT CDS complement(1827871..1829370)
FT /colour=7
FT /product="carboxylic acid transmembrane transporter Tna1"
FT /product="plasma membrane carboxylic acid transmembrane
FT transporter Tna1"
FT /systematic_id="SPAC1002.16c"
FT /primary_name="tna1"
FT /db_xref="SPD:24/24C10"
Expand Down Expand Up @@ -67286,6 +67286,8 @@ FT /controlled_curation="term=species distribution, conserved
FT in metazoa; date=20161031"
FT /controlled_curation="term=species distribution, conserved
FT in vertebrates; date=20161031"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20240818"
FT /product="mitochondrial DUF4536, human DMAC1 ortholog,
FT possibly has a general role in mitochondrial complex
FT assembly"
Expand Down Expand Up @@ -87486,8 +87488,8 @@ FT condition=FYECO:0000126; during=GO:0072690; score=12.4705;
FT db_xref=PMID:30566651"
FT CDS 5454901..5456424
FT /colour=7
FT /product="carboxylic acid transmembrane transporter
FT (predicted)"
FT /product="plasma membrane carboxylic acid transmembrane
FT transporter"
FT /systematic_id="SPAC1039.04"
FT /db_xref="SPD:24/24G02"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down
30 changes: 16 additions & 14 deletions data/chromosome2.contig
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Expand Up @@ -1824,8 +1824,8 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=57.510700; db_xref=PMID:30566651"
FT CDS 168671..170119
FT /colour=7
FT /product="carboxylic acid transmembrane transporter
FT (predicted)"
FT /product="plasma membrane carboxylic acid transmembrane
FT transporter"
FT /db_xref="SPD:23/23D01"
FT /systematic_id="SPBC1683.12"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -35356,7 +35356,7 @@ FT /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT condition=FYECO:0000126; during=GO:0072690;
FT score=170.104000; db_xref=PMID:30566651"
FT CDS complement(join(2218540..2218826,2218874..2218935,2218993..2219047,2219094..2219196))
FT /product="nucleolar RNA binding protein, human KNOP1
FT /product="nucleolar RNA binding protein, human SMAP
FT ortholog, implicated in mRNA processing"
FT /systematic_id="SPBC14C8.19"
FT /colour=10
Expand All @@ -35372,15 +35372,17 @@ FT in fungi; 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 in eukaryotes; db_xref=Pfam:PF15477; date=20140815"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20140815"
FT /controlled_curation="term=human KNOP1 ortholog;
FT date=20140816"
FT in eukaryotes only; db_xref=Pfam:PF15477; date=20140815"
FT /controlled_curation="term=human SMAP ortholog;
FT db_xref=Pfam:PF15477; date=20240816"
FT /controlled_curation="term=species distribution, conserved
FT in vertebrates; date=20140819"
FT in vertebrates; db_xref=Pfam:PF15477; date=20140819"
FT /controlled_curation="term=species distribution, conserved
FT in metazoa; date=20140819"
FT in metazoa; db_xref=Pfam:PF15477; date=20140819"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20140819"
FT 5'UTR complement(2219197..2219221)
FT /systematic_id="SPBC14C8.19"
FT /db_xref="PMID:30566651"
Expand Down Expand Up @@ -43721,7 +43723,7 @@ FT score=8.377430; db_xref=PMID:30566651"
FT CDS 2729258..2730613
FT /EC_number="3.4.13.-"
FT /colour=10
FT /product="X-Pro dipeptidase (predicted)"
FT /product="X-Pro dipeptidase"
FT /synonym="SPBC4F6.19c"
FT /synonym="ppp52"
FT /db_xref="SPD:21/21A09"
Expand All @@ -43733,14 +43735,14 @@ FT in fungi; date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in vertebrates; date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in metazoa; date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20170210"
FT /controlled_curation="term=species distribution, conserved
FT in archaea; date=20170210"
FT /controlled_curation="term=misc, removed the human
FT ortholog because XPNPEP1 and XPNPEP1 are fra1, although
FT this could be a divergent paralog of fra1; date=20240817"
FT /primary_name="xpa1"
FT /note="note that I "
FT 3'UTR 2730614..2730774
FT /systematic_id="SPBC18A7.01"
FT /db_xref="PMID:21511999"
Expand Down
2 changes: 1 addition & 1 deletion data/chromosome3.contig
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Expand Up @@ -6030,7 +6030,7 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=214.831000; db_xref=PMID:30566651"
FT CDS 430788..431639
FT /colour=12
FT /product="cell surface membrane anchored protein, proably
FT /product="cell surface membrane anchored protein, probably
FT carbohydrate binding domain"
FT /db_xref="SPD:11/11C01"
FT /systematic_id="SPCC306.11"
Expand Down
Binary file modified data/genome.pickle
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34 changes: 17 additions & 17 deletions results/allele_auto_fix.tsv
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@@ -1,21 +1,21 @@
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-3 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-18 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
SPAC18G6.02c SPAC18G6.02c:allele-17 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-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-103 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-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-18 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
SPAC977.10 SPAC977.10:allele-100 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-57 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-22 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-27 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
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D197N,D197DN multi_shift_fix D366|D366 3 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 D219N,D219DN multi_shift_fix D366|D366 4 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 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-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-8 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
SPBC428.08c SPBC428.08c:allele-16 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
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D197DN,D197N multi_shift_fix D366|D366 3 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 D219DN,D219N multi_shift_fix D366|D366 4 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 D282DN,D282N 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 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-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
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