Mercurial > repos > davidvanzessen > experimental_design_igg

comparison experimental_design.py @ 3:a558fed92bcf draft default tip

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author davidvanzessen
date Thu, 10 Jul 2014 07:25:10 -0400
parents f2c4c7151016
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2:f2c4c7151016 3:a558fed92bcf
12 if arg.find("/") is -1: 12 if arg.find("/") is -1:
13 patients[sample_id] = files 13 patients[sample_id] = files
14 files = [] 14 files = []
15 sample_id = arg 15 sample_id = arg
16 else: 16 else:
17 df = pd.read_csv(arg, sep="\t") 17 df = pd.read_csv(arg, sep="\t", dtype=object)
18 if "Functionality" in list(df.columns.values): 18 if "Functionality" in list(df.columns.values):
19 df["VDJ Frame"][df["Functionality"] != "productive"] = "In-frame with stop codon" 19 df["VDJ Frame"][df["Functionality"] != "productive"] = "In-frame with stop codon"
20 imgt_files += 1 20 imgt_files += 1
21 else: 21 else:
22 blast_files += 1 22 blast_files += 1