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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Dec 24, 2023
1 parent ae9d277 commit 9319e38
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Showing 10 changed files with 11,542 additions and 11,545 deletions.
10,055 changes: 5,028 additions & 5,027 deletions data/alleles.tsv
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10 changes: 6 additions & 4 deletions data/chromosome1.contig
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Expand Up @@ -15721,8 +15721,7 @@ FT /systematic_id="SPNCRNA.706"
FT /product="non-coding RNA"
FT CDS 1028316..1029797
FT /colour=7
FT /product="succinate-semialdehyde dehydrogenase
FT (predicted)"
FT /product="succinate-semialdehyde dehydrogenase Ssd2"
FT /systematic_id="SPAC139.05"
FT /db_xref="SPD:23/23H06"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand All @@ -15739,6 +15738,7 @@ 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"
FT /primary_name="ssd2"
FT 3'UTR 1029798..1029993
FT /systematic_id="SPAC139.05"
FT /db_xref="PMID:21511999"
Expand Down Expand Up @@ -27679,7 +27679,7 @@ FT /controlled_curation="term=orthologous to S. cerevisiae
FT YGL242C; date=19700101"
FT /controlled_curation="term=human OSTF1 ortholog;
FT db_xref=PMID:37163016; date=20121025"
FT /controlled_curation="term=name descirption, ANKyrin
FT /controlled_curation="term=name description, ANKyrin
FT repeats; date=20230302"
FT /db_xref="SPD:43/43D12"
FT /primary_name="ank1"
Expand Down Expand Up @@ -27714,6 +27714,7 @@ FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20090202"
FT /primary_name="dal81"
FT lncRNA 1747132..1749810
FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.2782"
Expand Down Expand Up @@ -28980,7 +28981,7 @@ FT /db_xref="PMID:21511999"
FT CDS complement(1818695..1820191)
FT /colour=7
FT /product="succinate-semialdehyde dehydrogenase [NAD(P)+]
FT (predicted)"
FT Ssd1"
FT /systematic_id="SPAC1002.12c"
FT /controlled_curation="term=orthologous to S. cerevisiae
FT YBR006W; date=19700101"
Expand All @@ -29001,6 +29002,7 @@ FT updated; db_xref=PMID:21511999; date=20110311"
FT /controlled_curation="term=warning, gene structure
FT updated; date=20220401"
FT /db_xref="SPD:24/24B12"
FT /primary_name="ssd1"
FT 5'UTR complement(1820192..1820272)
FT /systematic_id="SPAC1002.12c"
FT /db_xref="PMID:30566651"
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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-3 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
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-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-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-3 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-101 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-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-94 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-14 rpb1-CTD-P3A(r2-r29-2) CTD-P3A(r2-r29-2) amino_acid_insertion_and_mutation amino_acid_mutation type_error CTD-P3A(r2-r29-2) amino_acid_mutation:CTD PMID:32282918,PMID:33579781,PMID:34389684
SPBC28F2.12 SPBC28F2.12:allele-26 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-24 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-19 rpb1-CTD-P3A(r2-r29-2) CTD-P3A(r2-r29-2) amino_acid_insertion_and_mutation amino_acid_mutation type_error CTD-P3A(r2-r29-2) amino_acid_mutation:CTD PMID:32282918,PMID:33579781,PMID:34389684
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-11 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-15 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-2 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
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-3 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-1 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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