Is it possible to add the 'Gene' and peptide 'POSITION(S)' info corresponding to each genomic coordinate using MapUniProtFeatures

[wunalahu2]

Hi , lindenb I've successfully run MapUniProtFeatures ,and the top 10 line is exactly the same as in Example shown in http://lindenb.github.io/jvarkit/MapUniProtFeatures.html. My question is 'is it possible to add the 'Gene' and peptide 'POSITION(S)' info corresponding to each genomic coordinate , I want the result to be formatted like the following Gene POSITION(S) chr start end TYPE .... OR4F5 1-18 chr1 69090 69144 topological_domain .... OR4F5 19-42 chr1 69144 69216 transmembrane_region .... OR4F5 43-50 chr1 69216 69240 topological_domain .... The 'Gene' and peptide 'POSITION(S)' info should come from https://www.uniprot.org/ waiting for your reply ,thanks

[lindenb]

Hi, how about using bedtools intersect ?

[wunalahu2]

Thank you for your prompt reply. Using bedtools intersect may only get gene info for each genomic coordinate ,when I using WES bed as input . But I cannot get the peptide positions . My WES bed looks like as : chr1 69090 69240 target1 OR4F5:exon1 chr1 69240 69390 target2 OR4F5:exon1 chr1 69390 69540 target3 OR4F5:exon1 chr1 69540 69690 target4 OR4F5:exon1 chr1 69690 69840 target5 OR4F5:exon1 chr1 69840 69990 target6 OR4F5:exon1 chr1 69990 70008 target7 OR4F5:exon1

[wunalahu2]

Actually ,I want to add the genomic coordinates to each protein domain

[lindenb]

Sorry, I won't have the time to work on this.

[wunalahu2]

it doesn't matter，thank you very much for your prompt reply.