Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 38:539618b939bc draft

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Uploaded
author davidvanzessen
date Fri, 22 Jan 2016 10:44:50 -0500
parents 1d50685fd013
children 2e0a7c35082e
files imgt_loader/imgt_loader.r
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/imgt_loader/imgt_loader.r	Fri Jan 22 10:41:47 2016 -0500
+++ b/imgt_loader/imgt_loader.r	Fri Jan 22 10:44:50 2016 -0500
@@ -39,9 +39,9 @@
 
 out[,added_junction_columns] = junction[,added_junction_columns]
 
-out[,"Top V Gene"] = gsub("Homsap |Ratnor ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"]))
-out[,"Top D Gene"] = gsub("Homsap |Ratnor ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"]))
-out[,"Top J Gene"] = gsub("Homsap |Ratnor ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"]))
+out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"]))
+out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"]))
+out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"]))
 
 out = out[,c('Sequence.ID','JUNCTION.frame','Top V Gene','Top D Gene','Top J Gene','CDR1.Seq','CDR1.Length','CDR2.Seq','CDR2.Length','CDR3.Seq','CDR3.Length','CDR3.Seq.DNA','CDR3.Length.DNA','Strand','CDR3.Found.How','Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence','FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT','P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION')]