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more manual changes
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@manulera
manulera committed Jul 19, 2023
1 parent 658e426 commit 0ec33a2
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Showing 3 changed files with 43 additions and 27 deletions.
5 changes: 4 additions & 1 deletion manual_fixes_pombase/cannot_find.tsv
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Expand Up @@ -16,4 +16,7 @@ SPBC216.07c tor2-ts10 asked no A at position 1399, and there are several surroun
SPBC216.07c tor2-ts6 asked no K711, most likely this refers to K710.
SPAC19E9.02 fin1-KD K63R,N165A No N165, but there is a N156. I suspect that this could be scrambled numbers
SPAC29A4.08c prp19-W88P W88P closest W is at position 80
SPCC962.05 ast1-ND D158A,D160A,D179A,D181A oligonucleotides listed do not really align. They seem to be using a very different sequence. My guess it's maybe it refers to E132,D134 / D152,D154 / D159,D161
SPCC962.05 ast1-ND D158A,D160A,D179A,D181A oligonucleotides listed do not really align. They seem to be using a very different sequence. My guess it's maybe it refers to E132,D134 / D152,D154 / D159,D161
SPCC645.05c snipID G1000A From Jeffares paper, maybe it's outside of the gene?
SPBC365.06 pmt3-D18R D18R I cannot find a mention to this allele in the main text. pmt3 is mentioned only in the abstract.
SPCC16C4.11 pef1-N146S N146S Asked the authors
22 changes: 22 additions & 0 deletions manual_fixes_pombase/check_if_name_should_be_changed.py
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@@ -0,0 +1,22 @@
import pandas
import sys

manual_changes = pandas.read_csv(sys.argv[1], sep="\t", na_filter=False)
manual_changes.fillna('', inplace=True)

# only the ones that did not have a value in change_name_to
manual_changes = manual_changes[(manual_changes['change_name_to'] == '') & (manual_changes['change_description_to'] != '') & (manual_changes['allele_description'] != '')].copy()


def get_change_name_to(row):
new_description = row['change_description_to']
old_description = row['allele_description']
name = row['allele_name']
if old_description in name:
return name.replace(old_description, new_description)
return ''


manual_changes['change_name_to'] = manual_changes.apply(get_change_name_to, axis=1)
manual_changes = manual_changes[manual_changes['change_name_to'] != ''].copy()
manual_changes.to_csv('names_that_should_be_fixed.tsv', sep="\t", index=False)
43 changes: 17 additions & 26 deletions manual_fixes_pombase/manual_cannot_fix_new.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -111,15 +111,13 @@ SPBC1A4.03c top2-26-40/SV-delta-Xba amino acids 26-40 replaced by SV40 NLS seque
SPAC17G8.14c pck1-N(1-400) 401-998 partial_amino_acid_deletion PMID:11737264 401-988
SPCC320.13c ark1-NT 118-384 partial_amino_acid_deletion PMID:11950927 89-355
SPAC23C11.16 plo1-K65R K65R amino_acid_mutation PMID:12815070 K69R plo1-K69R described in cited publication PMID:11250892
SPNCRNA.214 C7U C7U nucleotide_mutation PMID:18157149 C234T from figure in paper, perhaps old coords complement(3084610..3086022)
SPNCRNA.214 U3G,A5U U3G,A5U nucleotide_mutation PMID:18157149 T230G,A232T from figure in paper, perhaps old coords complement(3084610..3086022)
SPNCRNA.214 C7U C7U nucleotide_mutation PMID:18157149 C234T ter1-C234T from figure in paper, perhaps old coords complement(3084610..3086022)
SPNCRNA.214 U3G,A5U U3G,A5U nucleotide_mutation PMID:18157149 T230G,A232T ter1-T230G,A232T from figure in paper, perhaps old coords complement(3084610..3086022)
SPCC550.05 nse1-15 120-236 partial_amino_acid_deletion PMID:21976700 120-232 typo in PomBase
SPCC550.05 nse1-C216S C1216S amino_acid_mutation PMID:21976700 C216S typo in PomBase
SPCC645.07 rgf1-Nes1* L865A,L866A,I867A amino_acid_mutation PMID:24478458 L875A,L876A,I877A typo in paper (I think), that's the only LLI sequence in the peptide
SPCC645.05c snipID G1000A nucleotide_mutation PMID:25665008
SPBC365.06 pmt3-D18R D18R amino_acid_mutation PMID:26221037
SPNCRNA.214 ter1-CATG/(A)4 CAUG1058AAAA nucleotide_mutation PMID:26305931
SPAC22G7.08 ppk8'-1 G474C nucleotide_mutation PMID:26730850
SPNCRNA.214 ter1-CATG/(A)4 CAUG1058AAAA nucleotide_mutation PMID:26305931 CATG-1052-AAAA
SPAC22G7.08 ppk8'-1 G474C nucleotide_mutation PMID:26730850 G67C
SPAC22G7.08 ppk8'-4 T471A,C472T,A476T nucleotide_mutation PMID:26730850 T64A,C65T,A69T
SPAC22G7.08 ppk8'-5 T471A,G473C nucleotide_mutation PMID:26730850 T64A,G66C
SPAC22G7.08 ppk8'-6 T471C,G473C nucleotide_mutation PMID:26730850 T64C,G66C
Expand All @@ -142,23 +140,16 @@ SPBC725.16 res1'-7 T976A,T977A,T979C nucleotide_mutation PMID:26730850 T229A,T23
SPBC725.16 res1'-B A1087T nucleotide_mutation PMID:26730850 A340T
SPBC725.16 res1'-D C1085G nucleotide_mutation PMID:26730850 C338G
SPBC725.16 res1'-E C1088G nucleotide_mutation PMID:26730850 C341G
SPBC354.05c sre2-MS+ G772L,N773L,Y775L 1-422,G772L,N773L,Y775L amino_acid_deletion_and_mutation PMID:27655872
SPBC354.05c sre2-MS+S760L 1-422,E760L amino_acid_deletion_and_mutation PMID:27655872
SPBC19C2.09 sre1-MP C-4865A, A-484T, C-483A, C-480A, A-479T, T-478A, C-528A, A-527T, G-526A, C-523A, A-522T, C-521A nucleotide_mutation PMID:28202541
SPCC31H12.08c ccr4- H665A amino_acid_mutation PMID:28404620
SPAC13A11.04c Y96C amino_acid_mutation PMID:29352077
SPAC10F6.09c psm3-Q1168E Q1168E amino_acid_mutation PMID:29735656
SPAC10F6.09c psm3-R1127I R1127I amino_acid_mutation PMID:29735656
SPCC5E4.04 cut1-L739S L379S amino_acid_mutation PMID:29735656
SPCC306.03c L318E amino_acid_mutation PMID:31072933
SPCC576.15c P320R amino_acid_mutation PMID:31072933
SPBC31E1.02c pmr1-W880->stop W800->stop nonsense_mutation PMID:31201205
SPCC16C4.11 pef1-N146S N146S amino_acid_mutation PMID:31895039
SPAC222.14c sey1-K53A K53A amino_acid_mutation PMID:32023460
SPNCRNA.899 SPNCRNA.899-G754C G754C nucleotide_mutation PMID:32142608
SPAC23C4.19 spt5(WT)7 T1T amino_acid_mutation PMID:32496538
SPBC31F10.14c hip3-Q808-stop Q808stop amino_acid_mutation PMID:34580178
SPBC8D2.03c hhf2-L83S L83S amino_acid_mutation PMID:34580178
SPAC6B12.07c pqr1-I84S I87S amino_acid_mutation PMID:35012333


SPBC354.05c sre2-MS+ G772L,N773L,Y775L 1-422,G772L,N773L,Y775L amino_acid_deletion_and_mutation PMID:27655872 1-422,G772L,N773L,Y774L sre2-MS+G772L,N773L,Y774L typo in PomBase
SPBC354.05c sre2-MS+S760L 1-422,E760L amino_acid_deletion_and_mutation PMID:27655872 1-422,S760L typo in PomBase
SPBC19C2.09 sre1-MP C-4865A, A-484T, C-483A, C-480A, A-479T, T-478A, C-528A, A-527T, G-526A, C-523A, A-522T, C-521A nucleotide_mutation PMID:28202541 CACCCCAT-(-528)-ATACCATA,CAGTCCAC-(-485)-ATATCATA
SPCC31H12.08c ccr4- H665A amino_acid_mutation PMID:28404620 H664A ccr4-H665A looked into the original cerevisiae paper figure (uses and old gene structure)
SPAC13A11.04c Y96C amino_acid_mutation PMID:29352077 Y95C ubp8-Y95C Error in the paper. Most likely refers to this residue, since the other referred Y residue is correct
SPCC5E4.04 cut1-L739S L379S amino_acid_mutation PMID:29735656 L739S typo in PomBase
SPCC306.03c L318E amino_acid_mutation PMID:31072933 K318E cnd2-K318E typo in PomBase
SPCC576.15c P320R amino_acid_mutation PMID:31072933 T320R ksg1-T320R typo in PomBase
SPBC31E1.02c pmr1-W880->stop W800->stop nonsense_mutation PMID:31201205 W880* pmr1-W880* typo in pombase
SPAC222.14c sey1-K53A K53A amino_acid_mutation PMID:32023460 K52A sey1-K52A Fig. 6 of https://doi.org/10.1016/j.cell.2009.05.025
SPNCRNA.899 SPNCRNA.899-G754C G754C nucleotide_mutation PMID:32142608 C754G Wrong orientation in the original description
SPBC31F10.14c hip3-Q808-stop Q808stop amino_acid_mutation PMID:34580178 C808* hip3-C808* typo in pombase
SPAC6B12.07c pqr1-I84S I87S amino_acid_mutation PMID:35012333 I84S typo in pombase

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