From 1562db032400d42e8aee6856eea3cd030d4824ee Mon Sep 17 00:00:00 2001 From: dormeight Date: Mon, 7 Oct 2019 09:33:26 +0100 Subject: [PATCH 1/2] modify to make it compatible with clonality.py add next(reader) to skip the headline and remove sample_1 or sample_2 from file names to locate the outputs of clonality.py --- compare.repertoires.py | 59 +++++++++++++++++++++--------------------- 1 file changed, 30 insertions(+), 29 deletions(-) diff --git a/compare.repertoires.py b/compare.repertoires.py index b96e617..c64f130 100644 --- a/compare.repertoires.py +++ b/compare.repertoires.py @@ -57,6 +57,7 @@ def file2dict(fileName): dict={} file=open(fileName,"r") reader=csv.reader(file) + next(reader)# skip the headline for row in reader: dict[row[0]]=int(row[1]) return dict @@ -84,27 +85,27 @@ def file2dict(fileName): print ("-----") print (sample_1,sample_2) +# remove "+ sample_1" or "+ sample_2" from the following lines +file_IGH_1=args.dir_1+"/IGH.cdr3.FREQ."+".csv" +file_IGH_2=args.dir_2+"/IGH.cdr3.FREQ."+".csv" -file_IGH_1=args.dir_1+"/IGH.cdr3.FREQ."+sample_1+".csv" -file_IGH_2=args.dir_2+"/IGH.cdr3.FREQ."+sample_2+".csv" +file_IGK_1=args.dir_1+"/IGK.cdr3.FREQ."+".csv" +file_IGK_2=args.dir_2+"/IGK.cdr3.FREQ."+".csv" -file_IGK_1=args.dir_1+"/IGK.cdr3.FREQ."+sample_1+".csv" -file_IGK_2=args.dir_2+"/IGK.cdr3.FREQ."+sample_2+".csv" +file_IGL_1=args.dir_1+"/IGL.cdr3.FREQ."+".csv" +file_IGL_2=args.dir_2+"/IGL.cdr3.FREQ."+".csv" -file_IGL_1=args.dir_1+"/IGL.cdr3.FREQ."+sample_1+".csv" -file_IGL_2=args.dir_2+"/IGL.cdr3.FREQ."+sample_2+".csv" +file_TCRA_1=args.dir_1+"/TCRA.cdr3.FREQ."+".csv" +file_TCRA_2=args.dir_2+"/TCRA.cdr3.FREQ."+".csv" -file_TCRA_1=args.dir_1+"/TCRA.cdr3.FREQ."+sample_1+".csv" -file_TCRA_2=args.dir_2+"/TCRA.cdr3.FREQ."+sample_2+".csv" +file_TCRB_1=args.dir_1+"/TCRB.cdr3.FREQ."+".csv" +file_TCRB_2=args.dir_2+"/TCRB.cdr3.FREQ."+".csv" -file_TCRB_1=args.dir_1+"/TCRB.cdr3.FREQ."+sample_1+".csv" -file_TCRB_2=args.dir_2+"/TCRB.cdr3.FREQ."+sample_2+".csv" +file_TCRD_1=args.dir_1+"/TCRD.cdr3.FREQ."+".csv" +file_TCRD_2=args.dir_2+"/TCRD.cdr3.FREQ."+".csv" -file_TCRD_1=args.dir_1+"/TCRD.cdr3.FREQ."+sample_1+".csv" -file_TCRD_2=args.dir_2+"/TCRD.cdr3.FREQ."+sample_2+".csv" - -file_TCRG_1=args.dir_1+"/TCRG.cdr3.FREQ."+sample_1+".csv" -file_TCRG_2=args.dir_2+"/TCRG.cdr3.FREQ."+sample_2+".csv" +file_TCRG_1=args.dir_1+"/TCRG.cdr3.FREQ."+".csv" +file_TCRG_2=args.dir_2+"/TCRG.cdr3.FREQ."+".csv" dict_IGH_1=file2dict(file_IGH_1) @@ -176,27 +177,27 @@ def file2dict(fileName): #VJ ----------------------------- +# also remove "+ sample_1" or "+ sample_2" from the following lines +file_IGH_1=args.dir_1+"/IGH.VJ.FREQ."+".csv" +file_IGH_2=args.dir_2+"/IGH.VJ.FREQ."+".csv" -file_IGH_1=args.dir_1+"/IGH.VJ.FREQ."+sample_1+".csv" -file_IGH_2=args.dir_2+"/IGH.VJ.FREQ."+sample_2+".csv" - -file_IGK_1=args.dir_1+"/IGK.VJ.FREQ."+sample_1+".csv" -file_IGK_2=args.dir_2+"/IGK.VJ.FREQ."+sample_2+".csv" +file_IGK_1=args.dir_1+"/IGK.VJ.FREQ."+".csv" +file_IGK_2=args.dir_2+"/IGK.VJ.FREQ."+".csv" -file_IGL_1=args.dir_1+"/IGL.VJ.FREQ."+sample_1+".csv" -file_IGL_2=args.dir_2+"/IGL.VJ.FREQ."+sample_2+".csv" +file_IGL_1=args.dir_1+"/IGL.VJ.FREQ."+".csv" +file_IGL_2=args.dir_2+"/IGL.VJ.FREQ."+".csv" -file_TCRA_1=args.dir_1+"/TCRA.VJ.FREQ."+sample_1+".csv" -file_TCRA_2=args.dir_2+"/TCRA.VJ.FREQ."+sample_2+".csv" +file_TCRA_1=args.dir_1+"/TCRA.VJ.FREQ."+".csv" +file_TCRA_2=args.dir_2+"/TCRA.VJ.FREQ."+".csv" -file_TCRB_1=args.dir_1+"/TCRB.VJ.FREQ."+sample_1+".csv" +file_TCRB_1=args.dir_1+"/TCRB.VJ.FREQ."+".csv" file_TCRB_2=args.dir_2+"/TCRB.VJ.FREQ."+sample_2+".csv" -file_TCRD_1=args.dir_1+"/TCRD.VJ.FREQ."+sample_1+".csv" -file_TCRD_2=args.dir_2+"/TCRD.VJ.FREQ."+sample_2+".csv" +file_TCRD_1=args.dir_1+"/TCRD.VJ.FREQ."+".csv" +file_TCRD_2=args.dir_2+"/TCRD.VJ.FREQ."+".csv" -file_TCRG_1=args.dir_1+"/TCRG.VJ.FREQ."+sample_1+".csv" -file_TCRG_2=args.dir_2+"/TCRG.VJ.FREQ."+sample_2+".csv" +file_TCRG_1=args.dir_1+"/TCRG.VJ.FREQ."+".csv" +file_TCRG_2=args.dir_2+"/TCRG.VJ.FREQ."+".csv" dict_IGH_1=file2dict(file_IGH_1) From ac276ced1d9944ad35d0bb633fead16bf38bc9e3 Mon Sep 17 00:00:00 2001 From: dormeight Date: Fri, 11 Oct 2019 09:31:51 +0100 Subject: [PATCH 2/2] Update compare.repertoires.py remove "sample_2" --- compare.repertoires.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/compare.repertoires.py b/compare.repertoires.py index c64f130..0eece98 100644 --- a/compare.repertoires.py +++ b/compare.repertoires.py @@ -191,7 +191,7 @@ def file2dict(fileName): file_TCRA_2=args.dir_2+"/TCRA.VJ.FREQ."+".csv" file_TCRB_1=args.dir_1+"/TCRB.VJ.FREQ."+".csv" -file_TCRB_2=args.dir_2+"/TCRB.VJ.FREQ."+sample_2+".csv" +file_TCRB_2=args.dir_2+"/TCRB.VJ.FREQ."+".csv" file_TCRD_1=args.dir_1+"/TCRD.VJ.FREQ."+".csv" file_TCRD_2=args.dir_2+"/TCRD.VJ.FREQ."+".csv"