Mercurial > repos > davidvanzessen > baseline_fasta_generator

comparison script_imgt.py @ 4:aa4b95abef11 draft

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Uploaded
author davidvanzessen
date Wed, 23 Jul 2014 10:13:05 -0400
parents be17e1e7dc2b
children 048f8cdbb6d2
comparison
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3:be17e1e7dc2b 4:aa4b95abef11
52 o.write(">>>IMGT\n") 52 o.write(">>>IMGT\n")
53 outputdic = dict() 53 outputdic = dict()
54 for line in i.readlines()[1:]: 54 for line in i.readlines()[1:]:
55 linesplt = line.split("\t") 55 linesplt = line.split("\t")
56 ref = filterGene(linesplt[1], vPattern) 56 ref = filterGene(linesplt[1], vPattern)
57 if not ref: 57 if not ref or not linesplt[2].rstrip():
58 continue 58 continue
59 if ref in outputdic: 59 if ref in outputdic:
60 outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())] 60 outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
61 else: 61 else:
62 outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())] 62 outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]