Problems with UniProt support
grayfall opened this issue · comments
I'm having problems converting amino-acid substitutions to genomic coordinates using UniProt identifiers, e.g.
$ transvar panno -i 'Q9BXW4:p.G126A' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
Q9BXW4:p.G126A CCDS31074 (protein_coding) MAP1LC3C - chr1:g.242159532C>G/c.377G>C/p.G126A inside_[cds_in_exon_4] CSQN=Missense;reference_codon=GGC;candidate_codons=GCA,GCC,GCG,GCT;candidate_mnv_variants=chr1:g.242159531_242159532delGCinsTG,chr1:g.242159531_242159532delGCinsCG,chr1:g.242159531_242159532delGCinsAG;source=CCDS
I'm getting the following output for quite a few proteins:
$ transvar panno -i 'Q99418:p.E156D' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
[wrap_exception] warning: seek out of range
Q99418:p.E156D . . . ././. . Error_seek out of range
[wrap_exception] warning: seek out of range
Q99418:p.E156D . . . ././. . Error_seek out of range
I've tried different locations and substitutions (e.g. -i 'Q99418:1'
) to no avail. Here are some more affected proteins: P04180, P45381, P45381, Q14289, P49916. Am I doing something wrong?
Thanks for reporting. I have
$ transvar panno -i 'Q99418:p.E156D' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
Q99418:p.E156D CCDS12722 (protein_coding) CYTH2 + chr19:g.48977195G>C/c.468G>C/p.E156D inside_[cds_in_exon_6] CSQN=Missense;reference_codon=GAG;candidate_codons=GAC,GAT;candidate_snv_variants=chr19:g.48977195G>T;source=CCDS
Q99418:p.E156D CCDS12722 (protein_coding) CYTH2 + chr19:g.48977195G>C/c.468G>C/p.E156D inside_[cds_in_exon_6] CSQN=Missense;reference_codon=GAG;candidate_codons=GAC,GAT;candidate_snv_variants=chr19:g.48977195G>T;source=CCDS
Have you tried with
transvar config --download_idmap
to get the Uniprot id maps?
Thanks,
@zwdzwd thanks for replying so quickly. Yes, I've downloaded the ID mapping, which is why some proteins do work.
(mutagenesis) $ transvar config --download_idmap
[downloading] ~/.cenvs/envs/mutagenesis/lib/python3.6/site-packages/transvar/transvar.download/uniprot.idmapping.txt.gz.idx ..Done (69.7 MB).
(mutagenesis) $ transvar panno -i 'Q99418:p.E156D' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
[wrap_exception] warning: seek out of range
Q99418:p.E156D . . . ././. . Error_seek out of range
[wrap_exception] warning: seek out of range
Q99418:p.E156D . . . ././. . Error_seek out of range
(mutagenesis) $ transvar panno -i 'Q9BXW4:p.G126A' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
Q9BXW4:p.G126A CCDS31074 (protein_coding) MAP1LC3C - chr1:g.242159532C>G/c.377G>C/p.G126A inside_[cds_in_exon_4] CSQN=Missense;reference_codon=GGC;candidate_codons=GCA,GCC,GCG,GCT;candidate_mnv_variants=chr1:g.242159531_242159532delGCinsTG,chr1:g.242159531_242159532delGCinsCG,chr1:g.242159531_242159532delGCinsAG;source=CCDS
(mutagenesis) $ transvar --version
TransVar Version 2.3.4.20161215
(mutagenesis) $ python --version
Python 3.6.6 :: Anaconda, Inc.
Hi @grayfall ,
Could you try the latest version? I tried with your Q99418 example and it seems to be working.
$ transvar panno -i 'Q99418:p.E156D' --uniprot --ccds
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
Q99418:p.E156D CCDS12722 (protein_coding) CYTH2 + chr19:g.48977195G>C/c.468G>C/p.E156D inside_[cds_in_exon_6] CSQN=Missense;reference_codon=GAG;candidate_codons=GAC,GAT;candidate_snv_variants=chr19:g.48977195G>T;source=CCDS
Q99418:p.E156D CCDS12722 (protein_coding) CYTH2 + chr19:g.48977195G>C/c.468G>C/p.E156D inside_[cds_in_exon_6] CSQN=Missense;reference_codon=GAG;candidate_codons=GAC,GAT;candidate_snv_variants=chr19:g.48977195G>T;source=CCDS
$ transvar config
Reference version: hg19
$ transvar --version
TransVar Version 2.4.0.20180701
$ python --version
Python 3.6.3 :: Anaconda, Inc.
@zwdzwd yes, the new release seems to work fine. Thank you.