# HG changeset patch
# User davidvanzessen
# Date 1395745166 14400
# Node ID 07a23652bc2a9ebc7c490b4e48741779176e1d5e
# Parent 03dbb4601b15135767d473a56f98adb991360676
Uploaded
diff -r 03dbb4601b15 -r 07a23652bc2a igblastmerge.py
--- a/igblastmerge.py Thu Jan 23 08:14:08 2014 -0500
+++ b/igblastmerge.py Tue Mar 25 06:59:26 2014 -0400
@@ -1,52 +1,44 @@
import sys
-# error
-def stop_err( msg ):
- sys.stderr.write( "%s\n" % msg )
- sys.exit()
-
-# main
-def main():
- args = sys.argv[1:-2]
-
- try:
- o = open(sys.argv[-1], 'w')
- i = open(args[1], 'r')
- separator = "\t"
- newline = "\n"
- line = i.readline()
- #write the header
- o.write(line[:line.rfind(newline)] + separator + "Sample" + separator + "Replicate" + newline)
- i.close()
-
- current = 1
- sampleID = args[0]
- count = 1
+import pandas as pd
- while True:
- print str(o)
- f = open(args[current], 'r')
- line = f.readline()
- line = f.readline()
- while line:
- o.write(line[:line.rfind(newline)] + separator + sampleID + separator + str(count) + newline)
- line = f.readline()
- f.close()
+def main():
+ patients = {}
+ files = []
+ sample_id = sys.argv[1]
+ imgt_files = 0
+ blast_files = 0
+ #organize files
+ for arg in sys.argv[2:-2]:
+ if arg.find("/") is -1:
+ patients[sample_id] = files
+ files = []
+ sample_id = arg
+ else:
+ df = pd.read_csv(arg, sep="\t")
+ if "Functionality" in list(df.columns.values):
+ df["VDJ Frame"][df["Functionality"] != "productive"] = "In-frame with stop codon"
+ imgt_files += 1
+ else:
+ blast_files += 1
+ files.append(df)
+ patients[sample_id] = files
+ columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'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', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb', u'Sample', u'Replicate']
+ if blast_files is not 0:
+ print "Has a parsed blastn file, using limited columns."
+ columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Sample', u'Replicate']
- if current >= (len(args) - 1):
- break
- if args[current + 1].find("/") is -1:
- sampleID = args[current + 1]
- current += 1
- count = 1
- else:
- count += 1
- current += 1
- o.close()
-
- except Exception, ex:
- stop_err('Error running new_column.py\n' + str(ex))
- sys.exit(0)
+ result = None
+ for patient_id, samples in patients.iteritems():
+ count = 1
+ for sample in samples:
+ sample['Sample'] = patient_id
+ sample['Replicate'] = str(count)
+ count += 1
+ if result is None:
+ result = sample[columns]
+ else:
+ result = result.append(sample[columns])
+ result.to_csv(sys.argv[-1], sep="\t", index=False, index_label="index")
if __name__ == "__main__":
- print sys.argv
main()
diff -r 03dbb4601b15 -r 07a23652bc2a igblastmerge.xml
--- a/igblastmerge.xml Thu Jan 23 08:14:08 2014 -0500
+++ b/igblastmerge.xml Tue Mar 25 06:59:26 2014 -0400
@@ -3,7 +3,7 @@
igblastmerge.py
#for $i, $f in enumerate($patients)
- $f.id
+ "$f.id"
#for $j, $g in enumerate($f.samples)
${g.sample}
#end for
@@ -12,7 +12,7 @@
--output $out_file
-
+