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fix gde1 alleles
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@manulera
manulera committed Jul 19, 2023
1 parent e647532 commit 19e8422
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Showing 2 changed files with 13 additions and 6 deletions.
6 changes: 5 additions & 1 deletion manual_fixes_pombase/get_cannot_fix_formatted.py
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Expand Up @@ -3,7 +3,11 @@
all_alleles = pandas.read_csv('../data/alleles.tsv', sep='\t', na_filter=False)
data = pandas.read_csv('../results/allele_cannot_fix_sequence_errors.tsv', sep='\t', na_filter=False)

already_fixed = pandas.read_csv('manual_cannot_fix_new.tsv', sep='\t', na_filter=False)
already_fixed = pandas.concat([
pandas.read_csv('manual_cannot_fix_new.tsv', sep='\t', na_filter=False),
pandas.read_csv('allele_manual_changes_formatted.tsv', sep='\t', na_filter=False),
pandas.read_csv('cannot_find.tsv', sep='\t', na_filter=False),
])

data = data[~data['allele_name'].isin(already_fixed['allele_name'])].copy()

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13 changes: 8 additions & 5 deletions manual_fixes_pombase/manual_cannot_fix_new.tsv
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Expand Up @@ -73,11 +73,14 @@ SPBC1718.07c zfs1-S164A,T1645A S164A,T164A amino_acid_mutation PMID:29084823 S16
SPBC8E4.01c pho84-TATA box mutant T-33C,A-32G,T-31C,A-30G,T-29C,A-28G,T-27C,A-26G nucleotide_mutation PMID:29414789 TATATATA-(-184)-CGCGCGCG negative coords in paper refer to the 5UTR, not the transcription start
SPNCRNA.1698 nc-tgp-+5_seb1_bs G521T,T543A,A554T,C569G,C578G nucleotide_mutation PMID:32499400 T543A,G549C,A554T,A560-T,T561A,C570G,G573A,C579G,T582A nucleotide_insertion_and_mutation
SPBC26H8.07c nda3noD U1347A,U1349C nucleotide_mutation PMID:34798057 T803A,T805C Serine 196 codon to Threo
SPAPB1E7.05 gde1-E845A,D847A L1M,E845A,D847A amino_acid_mutation PMID:35012333 E846A,D848A
SPAPB1E7.05 gde1-H810A,R811A L1M,H810A,R811A amino_acid_mutation PMID:35012333 H811A,R812A
SPAPB1E7.05 gde1-H860A L1M,H860A amino_acid_mutation PMID:35012333 H861A
SPAPB1E7.05 gde1-Y21F,K25A,N139A L1M,Y21F,K25A,N139A amino_acid_mutation PMID:35012333 Y22F,K26A,N140A
SPAPB1E7.05 gde1-R501G,G502V,Y503F,L504T,H505P,L506S,A507R(1-507) 508-1134,R501G,G502V,Y503F,L504T,H505P,L506S,A507R amino_acid_deletion_and_mutation PMID:35012333 510-1136,R503G,G504V,Y505F,L506T,H507P,L508S,A509R
SPAPB1E7.05 gde1-E845A,D847A L1M,E845A,D847A amino_acid_mutation PMID:35012333 E846A,D848A gde1-E846A,D848A
SPAPB1E7.05 gde1-H810A,R811A L1M,H810A,R811A amino_acid_mutation PMID:35012333 H811A,R812A gde1-H811A,R812A
SPAPB1E7.05 gde1-Y21F,K25A,N139A L1M,Y21F,K25A,N139A amino_acid_mutation PMID:35012333 Y22F,K26A,N140A gde1-Y22F,K26A,N140A
SPAPB1E7.05 gde1-R501G,G502V,Y503F,L504T,H505P,L506S,A507R(1-507) 508-1134,R501G,G502V,Y503F,L504T,H505P,L506S,A507R amino_acid_deletion_and_mutation PMID:35012333 510-1136,R503G,G504V,Y505F,L506T,H507P,L508S,A509R gde1-R503G,G504V,Y505F,L506T,H507P,L508S,A509R(1-509)
SPAPB1E7.05 gde1-(met1)E845A,D847A L1M,E845A,D847A amino_acid_mutation PMID:35012333 E846A,D848A gde1-E846A,D848A
SPAPB1E7.05 gde1-(met1)H810A,R811A L1M,H810A,R811A amino_acid_mutation PMID:35012333 H811A,R812A gde1-H811A,R812A
SPAPB1E7.05 gde1-(met1)H860A L1M,H860A amino_acid_mutation PMID:35012333 H861A gde1-H861A
SPAPB1E7.05 gde1-(met1)Y21F,K25A,N139A L1M,Y21F,K25A,N139A amino_acid_mutation PMID:35012333 Y22F,K26A,N140A gde1-Y22F,K26A,N140A
SPAC926.04c hsp90-EATA E34A,T179A amino_acid_mutation PMID:37120429 E34A,T172A coordinates were on the human protein, see Supp. Table 1
SPAC926.04c hsp90-EATK E34A,E384K amino_acid_mutation PMID:37120429 E34A,E367K coordinates were on the human protein, see Supp. Table 1
SPNCRNA.82 mrp1-B7 A370G nucleotide_mutation PMID:8887563 A371G
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