# HG changeset patch
# User davidvanzessen
# Date 1453477307 18000
# Node ID 1d50685fd0137fa4feb183504ca7aa3f2f16a0d0
# Parent  fd55088e48d24a02d1226d46440ec105cbef95fe
Uploaded

diff -r fd55088e48d2 -r 1d50685fd013 complete.sh
--- 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
diff -r fd55088e48d2 -r 1d50685fd013 imgt_loader/imgt_loader.r
--- 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')]