Skip to content

Commit

Permalink
updated to last revision
Browse files Browse the repository at this point in the history
  • Loading branch information
@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Nov 27, 2024
1 parent 225986f commit 46e9c8d
Show file tree
Hide file tree
Showing 11 changed files with 12,191 additions and 12,187 deletions.
10,708 changes: 5,354 additions & 5,354 deletions data/alleles.tsv
View file

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions data/chromosome1.contig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80976,8 +80976,8 @@ FT /systematic_id="SPNCRNA.4402"
FT /product="non-coding RNA"
FT CDS complement(join(5334980..5336152,5336212..5336298))
FT /colour=7
FT /product="mitochondrial translation factor (GTPase) Mtg2
FT (predicted)"
FT /product="mitochondrial large ribosomal subunit assembly
FT GTPase Mtg2"
FT /systematic_id="SPAP8A3.11c"
FT /controlled_curation="term=GTP1/OBG family; date=19700101"
FT /controlled_curation="term=species distribution, conserved
Expand Down
11 changes: 6 additions & 5 deletions data/chromosome2.contig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36955,10 +36955,10 @@ FT /systematic_id="SPBC21D10.08c"
FT /db_xref="PMID:21511999"
FT CDS complement(join(2433110..2433280,2433339..2433482))
FT /colour=7
FT /product="copper-binding protein of the mitochondrial
FT intermembrane space Cmc1 (predicted)"
FT /product="copper-binding protein involved in respiratory
FT complex assembly Cmc2"
FT /db_xref="SPD:02/02F04"
FT /primary_name="cmc1"
FT /primary_name="cmc2"
FT /systematic_id="SPBC21D10.07"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
Expand All @@ -36972,6 +36972,7 @@ FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20081110"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20081110"
FT /synonym="cmc1"
FT lncRNA complement(2433865..2434169)
FT /db_xref="PMID:29914874"
FT /db_xref="EMBL:AU012621"
Expand Down Expand Up @@ -39521,8 +39522,8 @@ FT /systematic_id="SPBC25B2.04c"
FT /db_xref="PMID:21511999"
FT CDS complement(join(2604654..2605021,2605113..2605731))
FT /colour=7
FT /product="mitochondrial translation factor (GTPase) Mtg1
FT (predicted)"
FT /product="mitochondrial large ribosomal subunit assembly
FT GTPase Mtg2"
FT /db_xref="SPD:16/16F10"
FT /systematic_id="SPBC25B2.04c"
FT /controlled_curation="term=species distribution, conserved
Expand Down
9 changes: 6 additions & 3 deletions data/chromosome3.contig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15692,8 +15692,8 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=4.962420; db_xref=PMID:30566651"
FT CDS join(1144468..1144646,1144709..1144799)
FT /systematic_id="SPCC4B3.20"
FT /product="cytochrome c oxidase assembly protein,
FT copper-binding, Cmc2"
FT /product="copper-binding protein involved in cytochrome c
FT oxidase assembly, Cmc1"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20090722"
FT /controlled_curation="term=species distribution, conserved
Expand All @@ -15708,9 +15708,12 @@ FT /controlled_curation="term=warning, new gene;
FT db_xref=PMID:21270388; date=20110131"
FT /controlled_curation="term=warning, new gene;
FT db_xref=PMID:21511999; date=20110311"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20241110"
FT /colour=7
FT /primary_name="cmc2"
FT /primary_name="cmc1"
FT /synonym="new24"
FT /synonym="cmc2"
FT intron 1144647..1144708
FT /controlled_curation="term=misc, confirmed intron"
FT /db_xref="PMID:21270388"
Expand Down
Binary file modified data/genome.pickle
View file
Binary file not shown.
32 changes: 16 additions & 16 deletions results/allele_auto_fix.tsv
View file
Original file line number Diff line number Diff line change
@@ -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-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-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
SPAC56E4.04c SPAC56E4.04c:allele-7 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-105 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
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-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-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-77 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-52 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-27 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-56 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-49 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
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
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
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-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
Loading

0 comments on commit 46e9c8d

Please sign in to comment.