Mercurial > repos > davidvanzessen > mutation_analysis

comparison gene_identification.py @ 64:0fdd90f7c654 draft

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Uploaded
author davidvanzessen
date Fri, 01 Apr 2016 08:54:24 -0400
parents 4262e880472d
children b869a126e2c4
comparison
equal deleted inserted replaced
63:a7381fd96dad 64:0fdd90f7c654
23 seqIndex = 0 23 seqIndex = 0
24 24
25 with open(infile, 'r') as f: #read all sequences into a dictionary as key = ID, value = sequence 25 with open(infile, 'r') as f: #read all sequences into a dictionary as key = ID, value = sequence
26 for line in f: 26 for line in f:
27 total += 1 27 total += 1
28 linesplt = line.split("\t")
28 if first: 29 if first:
29 linesplt = line.split("\t") 30 print "linesplt", linesplt
30 IDIndex = linesplt.index("Sequence ID") 31 IDIndex = linesplt.index("Sequence ID")
31 seqIndex = linesplt.index("Sequence") 32 seqIndex = linesplt.index("Sequence")
32 first = False 33 first = False
33 continue 34 continue
34 linesplt = line.split("\t") 35
35 ID = linesplt[IDIndex] 36 ID = linesplt[IDIndex]
36 if len(linesplt) < 28: #weird rows without a sequence 37 if len(linesplt) < 28: #weird rows without a sequence
37 dic[ID] = "" 38 dic[ID] = ""
38 else: 39 else:
39 dic[ID] = linesplt[seqIndex] 40 dic[ID] = linesplt[seqIndex]