Mercurial > repos > davidvanzessen > argalaxy_tools

comparison experimental_design/experimental_design.py @ 0:afe85eb6572e draft

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author davidvanzessen
date Mon, 29 Aug 2016 05:41:20 -0400
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-1:000000000000 0:afe85eb6572e
1 import sys
2 import pandas as pd
3
4 def main():
5 patients = {}
6 files = []
7 sample_id = sys.argv[1]
8 imgt_files = 0
9 blast_files = 0
10 #organize files
11 for arg in sys.argv[2:-2]:
12 if arg.find("/") is -1:
13 patients[sample_id] = files
14 files = []
15 sample_id = arg
16 else:
17 df = pd.read_csv(arg, sep="\t", dtype=object, error_bad_lines=False)
18 if "Functionality" in list(df.columns.values):
19 df["VDJ Frame"][df["Functionality"] != "productive"] = "In-frame with stop codon"
20 imgt_files += 1
21 else:
22 blast_files += 1
23 files.append(df)
24 patients[sample_id] = files
25 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',
26 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 %',
27 'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT',
28 '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',
29 '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']
30 if "N-REGION-nt nb" in files[0].columns:
31 columns.insert(30, "N-REGION-nt nb")
32 if blast_files is not 0:
33 print "Has a parsed blastn file, using limited columns."
34 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']
35
36 result = None
37 for patient_id, samples in patients.iteritems():
38 count = 1
39 for sample in samples:
40 sample['Sample'] = patient_id
41 sample['Replicate'] = str(count)
42 count += 1
43 if result is None:
44 result = sample[columns]
45 else:
46 result = result.append(sample[columns])
47 result.to_csv(sys.argv[-1], sep="\t", index=False, index_label="index")
48
49 if __name__ == "__main__":
50 main()