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modify to make it compatible with clonality.py #38

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modify to make it compatible with clonality.py #38

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1562db0
modify to make it compatible with clonality.py
dormeight Oct 7, 2019
ac276ce
Update compare.repertoires.py
dormeight Oct 11, 2019
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59 changes: 30 additions & 29 deletions compare.repertoires.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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"
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Is there a reason you didn't take out the sample_2 in this line?

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oh,my god. I forgot to remove these ones. all sample_1 or sample_2 should be removed

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@aaronkarlsberg aaronkarlsberg Oct 27, 2019 •
edited
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Great! @mandricigor could you modify the script to amend these two lines as well and create a new pull request?
@smangul1 I don't have authorization to merge a pull request with the master branch. Can you approve it and/or add me as a contributor?

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I merged these changes with the Mangul USC lab fork.
@mandricigor, I recommend merging this patch into your fork.
@dormeight made a good fix.


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)
Expand Down