Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 37:1d50685fd013 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 22 Jan 2016 10:41:47 -0500 |
| parents | fd55088e48d2 |
| children | 539618b939bc |
| files | complete.sh imgt_loader/imgt_loader.r |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/complete.sh Fri Jan 22 10:22:24 2016 -0500 +++ b/complete.sh Fri Jan 22 10:41:47 2016 -0500 @@ -60,7 +60,7 @@ echo "<tr><td>-----------------------------------</td></tr>" >> $html echo "<tr><td>merging</td></tr>" >> $html -python $dir/experimental_design/experimental_design.py ${mergerInput[*]} --output $PWD/merged.txt +bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt echo "<tr><td>done</td></tr>" >> $html echo "<tr><td>-----------------------------------</td></tr>" >> $html
--- a/imgt_loader/imgt_loader.r Fri Jan 22 10:22:24 2016 -0500 +++ b/imgt_loader/imgt_loader.r Fri Jan 22 10:41:47 2016 -0500 @@ -39,9 +39,9 @@ out[,added_junction_columns] = junction[,added_junction_columns] -out[,"Top V Gene"] = gsub("Homsap ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"])) -out[,"Top D Gene"] = gsub("Homsap ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"])) -out[,"Top J Gene"] = gsub("Homsap ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"])) +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 = 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')]