Mercurial > repos > cmonjeau > stacks

comparison stacks.py @ 3:0e0ff9e9c761 default tip

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fix inputs clean name
author cmonjeau
date Mon, 28 Sep 2015 13:21:35 +0000
parents d6ba40f6c824
children
comparison
equal deleted inserted replaced
2:c9e10e0d6c10 3:0e0ff9e9c761
33 33
34 tab_files=collections.OrderedDict() 34 tab_files=collections.OrderedDict()
35 for line in open(input_config, "r").readlines(): 35 for line in open(input_config, "r").readlines():
36 if line.strip() != '': 36 if line.strip() != '':
37 extract=line.strip().split("::") 37 extract=line.strip().split("::")
38 tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] 38 tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
39 39
40 # tabfiles[name]-> path 40 # tabfiles[name]-> path
41 return tab_files 41 return tab_files
42 42
43 43
45 45
46 tab_files=collections.OrderedDict() 46 tab_files=collections.OrderedDict()
47 for line in open(input_config, "r").readlines(): 47 for line in open(input_config, "r").readlines():
48 if line.strip() != '': 48 if line.strip() != '':
49 extract=line.strip().split("::") 49 extract=line.strip().split("::")
50 parse_name=re.search("^STACKS.*\((.*\.[ATCG]*\.fq)\)$", extract[0]) 50 parse_name=re.search("STACKS.*\((.*\.[ATCG]*).*\)$", extract[0])
51 # rename galaxy name in a short name 51 # rename galaxy name in a short name
52 if parse_name: 52 if parse_name:
53 extract[0]=parse_name.groups(1)[0] 53 extract[0]=parse_name.groups(1)[0]
54 54
55 tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1] 55 tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
56 56
57 # tabfiles[name]-> path 57 # tabfiles[name]-> path
58 return tab_files 58 return tab_files
59 59
60 60