Mercurial > repos > cropgeeks > flapjack

comparison FlapjackProject.py @ 81:819fdece454a draft

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Uploaded
author cropgeeks
date Wed, 07 Mar 2018 06:19:21 -0500
parents 7f0f361efcc0
children 348ad93dab47
comparison
equal deleted inserted replaced
80:7f0f361efcc0 81:819fdece454a
46 temp_parents = parents 46 temp_parents = parents
47 header = '' 47 header = ''
48 fj_header = '' 48 fj_header = ''
49 with open(my_file) as infile: 49 with open(my_file) as infile:
50 for line in infile: 50 for line in infile:
51 if line.lower().startswith("# fjfav"): 51 if line.startswith("# fjFav"):
52 favAlleleHeaders.append(line) 52 favAlleleHeaders.append(line)
53 continue 53 continue
54 elif line[:2] == '# ': 54 elif line[:2] == '# ':
55 fj_header += line 55 fj_header += line
56 elif header == '': 56 elif header == '':
180 else: 180 else:
181 name = key+'_'+sub 181 name = key+'_'+sub
182 name = str(name) 182 name = str(name)
183 sfile = filenames.get(samplefile + "_" + name) 183 sfile = filenames.get(samplefile + "_" + name)
184 gfile = filenames.get(genofile + "_" + name) 184 gfile = filenames.get(genofile + "_" + name)
185 gfile += '.tmp'
185 f = open(gfile, "a+") 186 f = open(gfile, "a+")
186 for fav in favAlleleHeaders: 187 for fav in favAlleleHeaders:
187 f.write(fav) 188 f.write(fav)
188 gfile += '.tmp' 189 f.close()
189 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C'] 190 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C']
190 if qtlfile: 191 if qtlfile:
191 cmd += ['-q',qtlfile] 192 cmd += ['-q',qtlfile]
192 if mapfile: 193 if mapfile:
193 cmd += ['-m',mapfile] 194 cmd += ['-m',mapfile]