Mercurial > repos > cropgeeks > flapjack

comparison FlapjackProject.py @ 79:df76e58799e7 draft

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Uploaded
author cropgeeks
date Wed, 07 Mar 2018 05:02:02 -0500
parents 6ace5881c494
children 7f0f361efcc0
comparison
equal deleted inserted replaced
78:3f84a298c6ca 79:df76e58799e7
37 PROFILE = 0 37 PROFILE = 0
38 38
39 parents = {} 39 parents = {}
40 40
41 filenames = {} 41 filenames = {}
42
43 favAlleleHeaders = []
42 44
43 def splitfile(my_file, sample_data, isSample): 45 def splitfile(my_file, sample_data, isSample):
44 temp_parents = parents 46 temp_parents = parents
45 header = '' 47 header = ''
46 fj_header = '' 48 fj_header = ''
47 with open(my_file) as infile: 49 with open(my_file) as infile:
48 for line in infile: 50 for line in infile:
49 if line[:2] == '# ': 51 if line.lower().startswith("# fjfav"):
52 favAlleleHeaders.append(line)
53 continue
54 elif line[:2] == '# ':
50 fj_header += line 55 fj_header += line
51 elif header == '': 56 elif header == '':
52 if fj_header == '': 57 if fj_header == '':
53 fj_header = '# fjFile = PHENOTYPE\n' 58 fj_header = '# fjFile = PHENOTYPE\n'
54 header_list = line.split('\t') 59 header_list = line.split('\t')
109 f.write('%s' % header) 114 f.write('%s' % header)
110 else : 115 else :
111 filename = filenames.get(my_file + "_" + group+'_'+cycle) 116 filename = filenames.get(my_file + "_" + group+'_'+cycle)
112 f=open(filename, "a+") 117 f=open(filename, "a+")
113 f.write('%s' % line) 118 f.write('%s' % line)
119 for key in filenames:
120 fname = filenames[key]
121 f = open(fname, "a+")
122 for fav in favAlleleHeaders:
123 f.write(fav)
114 124
115 125
116 126
117 def splitData(samplefile, genofile): 127 def splitData(samplefile, genofile):
118 # Split sample file # 128 # Split sample file #