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Arkadiy-GarberArkadiy-Garber
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‎FeGenie.py

Lines changed: 26 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -2594,19 +2594,19 @@ def delim(line):
25942594
normDict[i] = len(file.keys())
25952595

25962596
outHeat = open("%s/FeGenie-heatmap-data.csv" % (outDirectory), "w")
2597-
outHeat.write("X" + ',')
2597+
outHeat.write("X")
25982598
for i in sorted(Dict.keys()):
2599-
outHeat.write(i + ",")
2599+
outHeat.write("," + i)
26002600
outHeat.write("\n")
26012601

26022602
for i in cats:
26032603
outHeat.write(i + ",")
26042604
for j in sorted(Dict.keys()):
26052605
if not re.match(r'#', j):
26062606
if args.norm:
2607-
outHeat.write(str((len(Dict[j][i]) / int(normDict[j])) * float(args.inflation)) + ",")
2607+
outHeat.write("," + str((len(Dict[j][i]) / int(normDict[j])) * float(args.inflation)))
26082608
else:
2609-
outHeat.write(str(len(Dict[j][i])) + ",")
2609+
outHeat.write("," + str(len(Dict[j][i])))
26102610
outHeat.write("\n")
26112611

26122612
outHeat.close()
@@ -2675,16 +2675,16 @@ def delim(line):
26752675
Dict[cell][process].append(float(depthDict[cell][contig]))
26762676

26772677
outHeat = open("%s/FeGenie-%s-heatmap-data.csv" % (outDirectory, args.which_bams), "w")
2678-
outHeat.write("X" + ',')
2678+
outHeat.write("X")
26792679
for i in sorted(Dict.keys()):
2680-
outHeat.write(i + ",")
2680+
outHeat.write("," + i)
26812681
outHeat.write("\n")
26822682

26832683
for i in cats:
2684-
outHeat.write(i + ",")
2684+
outHeat.write(i)
26852685
for j in sorted(Dict.keys()):
26862686
if not re.match(r'#', j):
2687-
outHeat.write(str(SUM(Dict[j][i])) + ",")
2687+
outHeat.write("," + str(SUM(Dict[j][i])))
26882688
outHeat.write("\n")
26892689

26902690
outHeat.close()
@@ -2736,16 +2736,16 @@ def delim(line):
27362736
Dict[cell][process].append(float(depthDict[contig]))
27372737

27382738
outHeat = open("%s/FeGenie-heatmap-data.csv" % (outDirectory), "w")
2739-
outHeat.write("X" + ',')
2739+
outHeat.write("X")
27402740
for i in sorted(Dict.keys()):
2741-
outHeat.write(i + ",")
2741+
outHeat.write("," + i)
27422742
outHeat.write("\n")
27432743

27442744
for i in cats:
2745-
outHeat.write(i + ",")
2745+
outHeat.write(i)
27462746
for j in sorted(Dict.keys()):
27472747
if not re.match(r'#', j):
2748-
outHeat.write(str(SUM(Dict[j][i])) + ",")
2748+
outHeat.write("," + str(SUM(Dict[j][i])))
27492749
outHeat.write("\n")
27502750

27512751
outHeat.close()
@@ -2911,19 +2911,19 @@ def delim(line):
29112911
normDict[i] = len(file.keys())
29122912

29132913
outHeat = open("%s/FeGenie-heatmap-data.csv" % (outDirectory), "w")
2914-
outHeat.write("X" + ',')
2914+
outHeat.write("X")
29152915
for i in sorted(Dict.keys()):
2916-
outHeat.write(i + ",")
2916+
outHeat.write("," + i)
29172917
outHeat.write("\n")
29182918

29192919
for i in cats:
2920-
outHeat.write(i + ",")
2920+
outHeat.write(i)
29212921
for j in sorted(Dict.keys()):
29222922
if not re.match(r'#', j):
29232923
if args.norm:
2924-
outHeat.write(str((len(Dict[j][i]) / int(normDict[j])) * float(args.inflation)) + ",")
2924+
outHeat.write("," + str((len(Dict[j][i]) / int(normDict[j])) * float(args.inflation)))
29252925
else:
2926-
outHeat.write(str(len(Dict[j][i])) + ",")
2926+
outHeat.write("," + str(len(Dict[j][i])))
29272927
outHeat.write("\n")
29282928

29292929
outHeat.close()
@@ -2994,16 +2994,16 @@ def delim(line):
29942994
Dict[cell][process].append(float(depthDict[cell][contig]))
29952995

29962996
outHeat = open("%s/FeGenie-%s-heatmap-data.csv" % (outDirectory, args.which_bams), "w")
2997-
outHeat.write("X" + ',')
2997+
outHeat.write("X")
29982998
for i in sorted(Dict.keys()):
2999-
outHeat.write(i + ",")
2999+
outHeat.write("," + i)
30003000
outHeat.write("\n")
30013001

30023002
for i in cats:
3003-
outHeat.write(i + ",")
3003+
outHeat.write(i)
30043004
for j in sorted(Dict.keys()):
30053005
if not re.match(r'#', j):
3006-
outHeat.write(str(SUM(Dict[j][i])) + ",")
3006+
outHeat.write("," + str(SUM(Dict[j][i])))
30073007
outHeat.write("\n")
30083008

30093009
outHeat.close()
@@ -3056,16 +3056,16 @@ def delim(line):
30563056
Dict[cell][process].append(float(depthDict[contig]))
30573057

30583058
outHeat = open("%s/FeGenie-heatmap-data.csv" % (outDirectory), "w")
3059-
outHeat.write("X" + ',')
3059+
outHeat.write("X")
30603060
for i in sorted(Dict.keys()):
3061-
outHeat.write(i + ",")
3061+
outHeat.write("," + i)
30623062
outHeat.write("\n")
30633063

30643064
for i in cats:
3065-
outHeat.write(i + ",")
3065+
outHeat.write(i)
30663066
for j in sorted(Dict.keys()):
30673067
if not re.match(r'#', j):
3068-
outHeat.write(str(SUM(Dict[j][i])) + ",")
3068+
outHeat.write("," + str(SUM(Dict[j][i])))
30693069
outHeat.write("\n")
30703070

30713071
outHeat.close()
@@ -3089,7 +3089,7 @@ def delim(line):
30893089
os.system(
30903090
"Rscript --vanilla %s/dendro-heatmap.R %s/FeGenie-%s-heatmap-data.csv %s/" % (rscriptDir, outDirectory, args.which_bams, outDirectory))
30913091

3092-
os.system("mv %s/Fegenie-dotplot.tiff %s/Fegenie-%-dotplot.tiff" % (outDirectory, outDirectory, args.which_bams))
3092+
os.system("mv %s/Fegenie-dotplot.tiff %s/Fegenie-%s-dotplot.tiff" % (outDirectory, outDirectory, args.which_bams))
30933093

30943094
else:
30953095

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