Mercurial > repos > cropgeeks > flapjack

comparison FlapjackProject.py @ 80:7f0f361efcc0 draft

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Uploaded
author cropgeeks
date Wed, 07 Mar 2018 05:14:57 -0500
parents df76e58799e7
children 819fdece454a
comparison
equal deleted inserted replaced
79:df76e58799e7 80:7f0f361efcc0
114 f.write('%s' % header) 114 f.write('%s' % header)
115 else : 115 else :
116 filename = filenames.get(my_file + "_" + group+'_'+cycle) 116 filename = filenames.get(my_file + "_" + group+'_'+cycle)
117 f=open(filename, "a+") 117 f=open(filename, "a+")
118 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)
124 119
125 120
126 121
127 def splitData(samplefile, genofile): 122 def splitData(samplefile, genofile):
128 # Split sample file # 123 # Split sample file #
185 else: 180 else:
186 name = key+'_'+sub 181 name = key+'_'+sub
187 name = str(name) 182 name = str(name)
188 sfile = filenames.get(samplefile + "_" + name) 183 sfile = filenames.get(samplefile + "_" + name)
189 gfile = filenames.get(genofile + "_" + name) 184 gfile = filenames.get(genofile + "_" + name)
185 f = open(gfile, "a+")
186 for fav in favAlleleHeaders:
187 f.write(fav)
190 gfile += '.tmp' 188 gfile += '.tmp'
191 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C'] 189 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C']
192 if qtlfile: 190 if qtlfile:
193 cmd += ['-q',qtlfile] 191 cmd += ['-q',qtlfile]
194 if mapfile: 192 if mapfile: