Mercurial > repos > davidvanzessen > shm_csr

comparison baseline/script_imgt.py @ 32:4c5ba6b5d10d draft

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Uploaded
author davidvanzessen
date Thu, 15 Dec 2016 09:21:54 -0500
parents c33d93683a09
children 8728284105ee
comparison
equal deleted inserted replaced
31:fe44a905aee9 32:4c5ba6b5d10d
9 parser.add_argument("--id", help="ID to be used at the '>>>' line in the output") 9 parser.add_argument("--id", help="ID to be used at the '>>>' line in the output")
10 10
11 args = parser.parse_args() 11 args = parser.parse_args()
12 12
13 refdic = dict() 13 refdic = dict()
14 with open(args.ref, 'r') as ref: 14 with open(args.ref, 'rU') as ref:
15 currentSeq = "" 15 currentSeq = ""
16 currentId = "" 16 currentId = ""
17 for line in ref: 17 for line in ref:
18 if line[0] is ">": 18 if line[0] is ">":
19 if currentSeq is not "" and currentId is not "": 19 if currentSeq is not "" and currentId is not "":
35 35
36 #vPattern = re.compile(r"|".join(vPattern)) 36 #vPattern = re.compile(r"|".join(vPattern))
37 vPattern = re.compile("|".join(vPattern)) 37 vPattern = re.compile("|".join(vPattern))
38 38
39 def filterGene(s, pattern): 39 def filterGene(s, pattern):
40 s1 = s[s.find(" ") + 1:]
41 return s1[:s1.find(" ")]
42 """
40 if type(s) is not str: 43 if type(s) is not str:
41 return None 44 return None
42 res = pattern.search(s) 45 res = pattern.search(s)
43 if res: 46 if res:
44 return res.group(0) 47 return res.group(0)
45 return None 48 return None
46 49 """
47 50
48 51
49 currentSeq = "" 52 currentSeq = ""
50 currentId = "" 53 currentId = ""
51 first=True 54 first=True