Mercurial > repos > cropgeeks > flapjack

comparison FlapjackProject.py @ 77:6ace5881c494 draft

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Uploaded
author cropgeeks
date Mon, 26 Feb 2018 04:02:00 -0500
parents 84ce7c332dc4
children df76e58799e7
comparison
equal deleted inserted replaced
76:84ce7c332dc4 77:6ace5881c494
36 TESTRUN = 0 36 TESTRUN = 0
37 PROFILE = 0 37 PROFILE = 0
38 38
39 parents = {} 39 parents = {}
40 40
41 samplefiles = {} 41 filenames = {}
42 genotypefiles = {}
43 42
44 def splitfile(my_file, sample_data, isSample): 43 def splitfile(my_file, sample_data, isSample):
45 temp_parents = parents 44 temp_parents = parents
46 header = '' 45 header = ''
47 fj_header = '' 46 fj_header = ''
69 value = temp_parents[key] 68 value = temp_parents[key]
70 if dnarun in value: 69 if dnarun in value:
71 name = my_file + "_" + key 70 name = my_file + "_" + key
72 if isSample: 71 if isSample:
73 continue 72 continue
74 if name not in samplefiles: 73 if name not in filenames:
75 filename = tempfile.NamedTemporaryFile(delete=False).name 74 filename = tempfile.NamedTemporaryFile(delete=False).name
76 print("sample file %s has filename %s" % (name, filename)) 75 filenames[name] = filename
77 samplefiles[name] = filename
78 f = open(filename, "w") 76 f = open(filename, "w")
79 f.write('%s' % header) 77 f.write('%s' % header)
80 else: 78 else:
81 filename = samplefiles.get(name) 79 filename = filenames.get(name)
82 f=open(filename, "a+") 80 f=open(filename, "a+")
83 f.write('%s' % line) 81 f.write('%s' % line)
84 isParent = True 82 isParent = True
85 83
86 if isParent: 84 if isParent:
93 91
94 filename = tempfile.NamedTemporaryFile(delete=False).name 92 filename = tempfile.NamedTemporaryFile(delete=False).name
95 # get file name for genotype data 93 # get file name for genotype data
96 if isinstance(cycle, float) and math.isnan(cycle): 94 if isinstance(cycle, float) and math.isnan(cycle):
97 # save genotype data to file 95 # save genotype data to file
98 if my_file + "_" + group not in genotypefiles: 96 if my_file + "_" + group not in filenames:
99 genotypefiles[my_file + "_" + group] = filename 97 filenames[my_file + "_" + group] = filename
100 print("genotype file %s has filename %s" % (my_file + "_" + group, filename))
101 f = open(filename, "w") 98 f = open(filename, "w")
102 f.write('%s' % header) 99 f.write('%s' % header)
103 else : 100 else :
101 filename = filenames.get(my_file + "_" + group)
104 f=open(filename, "a+") 102 f=open(filename, "a+")
105 f.write('%s' % line) 103 f.write('%s' % line)
106 else: 104 else:
107 # save genotype data to file 105 # save genotype data to file
108 if group not in genotypefiles: 106 if my_file + "_" + group+'_'+cycle not in filenames:
109 genotypefiles[my_file + "_" + group+'_'+cycle] = filename 107 filenames[my_file + "_" + group+'_'+cycle] = filename
110 f = open(filename, "w") 108 f = open(filename, "w")
111 f.write('%s' % header) 109 f.write('%s' % header)
112 else : 110 else :
111 filename = filenames.get(my_file + "_" + group+'_'+cycle)
113 f=open(filename, "a+") 112 f=open(filename, "a+")
114 f.write('%s' % line) 113 f.write('%s' % line)
115 114
116 115
117 116
174 elif isinstance(sub, str) and not sub: 173 elif isinstance(sub, str) and not sub:
175 name = key 174 name = key
176 else: 175 else:
177 name = key+'_'+sub 176 name = key+'_'+sub
178 name = str(name) 177 name = str(name)
179 sfile = samplefiles.get(samplefile + "_" + name) 178 sfile = filenames.get(samplefile + "_" + name)
180 gfile = genotypefiles.get(genofile + "_" + name) 179 gfile = filenames.get(genofile + "_" + name)
181 gfile += '.tmp' 180 gfile += '.tmp'
182 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C'] 181 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C']
183 if qtlfile: 182 if qtlfile:
184 cmd += ['-q',qtlfile] 183 cmd += ['-q',qtlfile]
185 if mapfile: 184 if mapfile:
201 elif isinstance(sub, str) and not sub: 200 elif isinstance(sub, str) and not sub:
202 name = key 201 name = key
203 else: 202 else:
204 name = key+'_'+sub 203 name = key+'_'+sub
205 name = str(name) 204 name = str(name)
206 print("samplefile %s name %s" % (samplefile, name)) 205 sfile = filenames.get(samplefile + "_" + name)
207 sfile = samplefiles.get(samplefile + "_" + name) 206 gfile = filenames.get(genofile + "_" + name)
208 print("sfile %s" + sfile)
209 gfile = genotypefiles.get(genofile + "_" + name)
210 print("gfile %s" + gfile)
211 207
212 cmd = ['java','-jar',headerjar,sfile,gfile,gfile+'.tmp'] 208 cmd = ['java','-jar',headerjar,sfile,gfile,gfile+'.tmp']
213 call(cmd) 209 call(cmd)
214 210
215 def main(argv=None): 211 def main(argv=None):