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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Feb 19, 2025
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Showing 13 changed files with 12,383 additions and 12,384 deletions.
10,936 changes: 5,468 additions & 5,468 deletions data/alleles.tsv
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8 changes: 2 additions & 6 deletions data/chromosome1.contig
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Expand Up @@ -21524,7 +21524,7 @@ FT 3'UTR complement(1451843..1451956)
FT /systematic_id="SPAC3A12.17c"
FT /db_xref="PMID:21511999"
FT CDS complement(1451957..1453144)
FT /colour=2
FT /colour=10
FT /primary_name="cys12"
FT /product="cysteine synthase-like protein Cys12"
FT /synonym="cys1b"
Expand All @@ -21535,10 +21535,6 @@ FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in metazoa; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in vertebrates; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20081110"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20081110"
Expand Down Expand Up @@ -56140,7 +56136,7 @@ FT condition=FYECO:0000126; during=GO:0072690; score=27.2826;
FT db_xref=PMID:30566651"
FT CDS join(3688782..3688806,3689322..3689638,3689722..3690441,3690484..3691125)
FT /colour=7
FT /product="vacuolar/ prevavuolar endosome sodium/potassium
FT /product="vacuolar/ prevacuolar endosome sodium/potassium
FT ion/proton antiporter Nhx1"
FT /systematic_id="SPAC15A10.06"
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 @@ -1608,7 +1608,8 @@ FT CDS complement(160461..162155)
FT /EC_number="1.16.1.7"
FT /colour=2
FT /primary_name="frp1"
FT /product="plasma membrane ferric-chelate reductase Frp1"
FT /product="plasma membrane ferric-chelate reductase (NADPH)
FT Frp1"
FT /db_xref="SPD:35/35C11"
FT /systematic_id="SPBC1683.09c"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -4601,7 +4602,7 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=31.750800; db_xref=PMID:30566651"
FT CDS 348314..350059
FT /colour=7
FT /product="transmembrane transporter (predicted)"
FT /product="polyamine transmembrane transporter family"
FT /db_xref="SPD:35/35H12"
FT /systematic_id="SPBC1271.10c"
FT /controlled_curation="term=species distribution, conserved
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6 changes: 3 additions & 3 deletions data/chromosome3.contig
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Expand Up @@ -3345,7 +3345,7 @@ FT /systematic_id="SPNCRNA.6766"
FT /product="non-coding RNA"
FT CDS 260437..261732
FT /colour=7
FT /product="transmembrane transporter (predicted)"
FT /product="malate transmembrane transporter family"
FT /db_xref="SPD:22/22E05"
FT /systematic_id="SPCC794.06"
FT /controlled_curation="term=species distribution, no
Expand Down Expand Up @@ -5997,9 +5997,9 @@ FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.6855"
FT /product="non-coding RNA"
FT CDS 445404..446051
FT /colour=7
FT /colour=2
FT /product="Hrd1 ubiquitin ligase complex, CUE domain
FT protein Cue1 (predicted)"
FT protein Cue1"
FT /db_xref="SPD:07/07E01"
FT /systematic_id="SPCC4G3.13c"
FT /controlled_curation="term=CUE domain protein;
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10 changes: 5 additions & 5 deletions data/coordinate_changes_dict.json
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Expand Up @@ -244,11 +244,11 @@
],
"SPAC144.11": [
{
"revision": "10412",
"new_coord": "complement(4674612..4675070)",
"old_coord": "4674612..4675070",
"new_alignment": "LEFTKLFGTLGVLNDTENVKTNGLAQRTALTNSDNITLVDTESRRDMGSQVLVTLLITIVLGNKVQILTTDDDGTVHLGRNNSTSQNTTTDGYLTNKRALLVNILTVDSFGRGLESQTDILVPTTSSALLGVLEDVGLLLEGTLTLNDKLGSH---------------------------------------------------------------------------------------------------------------------------------------------------------",
"old_alignment": "---------------------------------------------------------------------------------------------------------------------------------------------------------MATELVVQSERAFQKQPHIFQNAKKGAGRRWYKDVGLGFKTPAEAIYGEYVDKKCPFVGQVSIRGRILTGTVVSTKMHRTIIIRREYLHFIPKYNRYEKRHKNLAAHVSPAFRINEGDVVTVGQCRPLSKTVRFNVLRVVKHTEGPKQFGKF*"
"revision": "10513",
"new_coord": "4674612..4675070",
"old_coord": "complement(4674612..4675070)",
"new_alignment": "MATELVVQSERAFQKQPHIFQNAKKGAGRRWYKDVGLGFKTPAEAIYGEYVDKKCPFVGQVSIRGRILTGTVVSTKMHRTIIIRREYLHFIPKYNRYEKRHKNLAAHVSPAFRINEGDVVTVGQCRPLSKTVRFNVLRVVKHTEGPKQFGKF*---------------------------------------------------------------------------------------------------------------------------------------------------------",
"old_alignment": "---------------------------------------------------------------------------------------------------------------------------------------------------------LEFTKLFGTLGVLNDTENVKTNGLAQRTALTNSDNITLVDTESRRDMGSQVLVTLLITIVLGNKVQILTTDDDGTVHLGRNNSTSQNTTTDGYLTNKRALLVNILTVDSFGRGLESQTDILVPTTSSALLGVLEDVGLLLEGTLTLNDKLGSH"
}
],
"SPAC144.17c": [
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Binary file modified data/genome.pickle
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2 changes: 2 additions & 0 deletions data/only_modified_coordinates.tsv
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@@ -1,4 +1,6 @@
revision user date chromosome systematic_id primary_name feature_type added_or_removed value
10513 vw253 2025-02-12 I SPAC144.11 rps1102 CDS added 4674612..4675070
10513 vw253 2025-02-12 I SPAC144.11 rps1102 CDS removed complement(4674612..4675070)
10412 vw253 2025-01-17 I SPAC144.11 rps1102 CDS added complement(4674612..4675070)
10412 vw253 2025-01-17 I SPAC144.11 rps1102 CDS removed 4674612..4675070
9820 vw253 2024-06-26 I SPSNORNA.18 snoU24 snoRNA added complement(5369613..5369691)
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22 changes: 11 additions & 11 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-3 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-11 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-22 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-6 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-91 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-54 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-57 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-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-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-117 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-6 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-13 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-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-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
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-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-6 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-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-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
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