|
65
|
1 #!/usr/bin/env python
|
|
|
2 # encoding: utf-8
|
|
|
3 '''
|
|
|
4 DNASampleSplitter -- shortdesc
|
|
|
5
|
|
|
6 DNASampleSplitter is a description
|
|
|
7
|
|
|
8 It defines classes_and_methods
|
|
|
9
|
|
|
10 @author: John Carlos Ignacia, Milcah, Yaw Nti-Addae
|
|
|
11
|
|
|
12 @copyright: 2017 Cornell University. All rights reserved.
|
|
|
13
|
|
|
14 @license: MIT License
|
|
|
15
|
|
|
16 @contact: yn259@cornell.edu
|
|
|
17 @deffield updated: Updated
|
|
|
18 '''
|
|
|
19
|
|
|
20 import sys
|
|
|
21 import os
|
|
|
22 import math
|
|
|
23 import pandas as pd
|
|
|
24
|
|
|
25 from optparse import OptionParser
|
|
|
26 from __builtin__ import str
|
|
|
27 from subprocess import call
|
|
|
28
|
|
|
29 __all__ = []
|
|
|
30 __version__ = 0.1
|
|
|
31 __date__ = '2017-06-20'
|
|
|
32 __updated__ = '2017-06-20'
|
|
|
33
|
|
|
34 DEBUG = 1
|
|
|
35 TESTRUN = 0
|
|
|
36 PROFILE = 0
|
|
|
37
|
|
|
38 parents = {}
|
|
|
39
|
|
|
40 def splitfile(my_file, sample_data):
|
|
|
41 header = ''
|
|
|
42 fj_header = ''
|
|
|
43 with open(my_file) as infile:
|
|
|
44 for line in infile:
|
|
|
45 if line[:2] == '# ':
|
|
|
46 fj_header += line
|
|
|
47 elif header == '':
|
|
|
48 if fj_header == '':
|
|
|
49 fj_header = '# fjFile = PHENOTYPE\n'
|
|
|
50 header_list = line.split('\t')
|
|
|
51 if header_list[0] != '':
|
|
|
52 header_list[0] = ''
|
|
|
53 line = "\t".join(header_list)
|
|
|
54 header = fj_header+line
|
|
|
55 else:
|
|
|
56 lst = line.split('\t')
|
|
|
57 dnarun = lst[0]
|
|
|
58 dnarun_data = sample_data[sample_data.dnarun_name == dnarun]
|
|
|
59 group = list(dnarun_data.dnasample_sample_group)[0]
|
|
|
60 cycle = list(dnarun_data.dnasample_sample_group_cycle)[0]
|
|
|
61
|
|
|
62 filename = my_file
|
|
|
63 isParent = False
|
|
|
64 for key in parents:
|
|
|
65 value = parents[key]
|
|
|
66 if dnarun in value:
|
|
|
67 filename = my_file+'_'+key+'.txt'
|
|
|
68 if not os.path.isfile(filename) :
|
|
|
69 f = open(filename, "w")
|
|
|
70 f.write('%s' % header)
|
|
|
71 else:
|
|
|
72 f=open(filename, "a+")
|
|
|
73 f.write('%s' % line)
|
|
|
74 isParent = True
|
|
|
75
|
|
|
76 if isParent:
|
|
|
77 continue
|
|
|
78
|
|
|
79 if isinstance(group, float) and math.isnan(group):
|
|
|
80 continue
|
|
|
81 else:
|
|
|
82 # get parent data #
|
|
|
83
|
|
|
84 # get file name for genotype data
|
|
|
85 if isinstance(cycle, float) and math.isnan(cycle):
|
|
|
86 filename += '_'+group+'.txt'
|
|
|
87 else:
|
|
|
88 filename += '_'+group+'_'+cycle+'.txt'
|
|
|
89
|
|
|
90 # save genotype data to file
|
|
|
91 if not os.path.isfile(filename) :
|
|
|
92 f = open(filename, "w")
|
|
|
93 f.write('%s' % header)
|
|
|
94 else :
|
|
|
95 f=open(filename, "a+")
|
|
|
96 f.write('%s' % line)
|
|
|
97
|
|
|
98 def splitData(samplefile, genofile):
|
|
|
99 # Split sample file #
|
|
|
100 sample_data = pd.read_table(samplefile, dtype='str')
|
|
|
101 group_list = sample_data.dnasample_sample_group.drop_duplicates()
|
|
|
102 for index, item in group_list.iteritems():
|
|
|
103 if isinstance(item, float):
|
|
|
104 if math.isnan(item):
|
|
|
105 continue
|
|
|
106 elif isinstance(item, str):
|
|
|
107 if not item:
|
|
|
108 continue
|
|
|
109 df = sample_data[sample_data.dnasample_sample_group == item]
|
|
|
110
|
|
|
111 # store dnaruns of parents in a dictionary
|
|
|
112 par1 = list(set(filter(lambda x: str(x) != 'nan', df.germplasm_par1)))
|
|
|
113 par2 = list(set(filter(lambda x: str(x) != 'nan', df.germplasm_par2)))
|
|
|
114 lst1 = list(sample_data.loc[sample_data.germplasm_name.isin(par1), 'dnarun_name'])
|
|
|
115 lst2 = list(sample_data.loc[sample_data.germplasm_name.isin(par2), 'dnarun_name'])
|
|
|
116 mergedlst = lst1 + lst2
|
|
|
117
|
|
|
118 subgroup_list = df.dnasample_sample_group_cycle.drop_duplicates()
|
|
|
119 for idx, sub in subgroup_list.iteritems():
|
|
|
120 if isinstance(sub, float):
|
|
|
121 if math.isnan(sub):
|
|
|
122 # df.to_csv(samplefile+"_"+item+".txt", index=None, na_rep='', sep="\t", mode="w", line_terminator="\n")
|
|
|
123 if not item in parents and mergedlst:
|
|
|
124 parents.update({item : mergedlst})
|
|
|
125 continue
|
|
|
126 elif isinstance(sub, str):
|
|
|
127 if not sub:
|
|
|
128 # df.to_csv(samplefile+"_"+item+".txt", index=None, na_rep='', sep="\t", mode="w", line_terminator="\n")
|
|
|
129 continue
|
|
|
130
|
|
|
131 subkey = item+'_'+sub
|
|
|
132 if not subkey in parents and mergedlst:
|
|
|
133 parents.update({subkey : lst1+lst2})
|
|
|
134 # df_sub = df[df.dnasample_sample_group_cycle == sub]
|
|
|
135 # df_sub.to_csv(samplefile+"_"+item+"_"+sub+".txt", index=None, na_rep='', sep="\t", mode="w", line_terminator="\n")
|
|
|
136
|
|
|
137 # Split genotype file based on sample information #
|
|
|
138 splitfile(samplefile, sample_data)
|
|
|
139 splitfile(genofile, sample_data)
|
|
|
140
|
|
|
141 def createProjectFile(groups, samplefile, genofile, jarfile, separator, missing, qtlfile, mapfile):
|
|
|
142 for key in groups:
|
|
|
143 sfile = samplefile+'_'+key+'.txt'
|
|
|
144 gfile = genofile+'_'+key+'.txt.tmp'
|
|
|
145 cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',genofile+'.flapjack','-S',separator,'-M',missing,'-n',key,'-q',qtlfile,'-m',mapfile]
|
|
|
146 call(cmd)
|
|
|
147
|
|
|
148 def createHeader(groups, samplefile, genofile, headerjar):
|
|
|
149 for key in groups:
|
|
|
150 sfile = samplefile+'_'+key+'.txt'
|
|
|
151 gfile = genofile+'_'+key+'.txt'
|
|
|
152 cmd = ['java','-jar',headerjar,sfile,gfile,gfile+'.tmp']
|
|
|
153 call(cmd)
|
|
|
154
|
|
|
155 def main(argv=None):
|
|
|
156 '''Command line options.'''
|
|
|
157
|
|
|
158 program_name = os.path.basename(sys.argv[0])
|
|
|
159 program_version = "v0.1"
|
|
|
160 program_build_date = "%s" % __updated__
|
|
|
161
|
|
|
162 program_version_string = '%%prog %s (%s)' % (program_version, program_build_date)
|
|
|
163 #program_usage = '''usage: spam two eggs''' # optional - will be autogenerated by optparse
|
|
|
164 program_longdesc = '''''' # optional - give further explanation about what the program does
|
|
|
165 program_license = "Copyright 2017 user_name (organization_name) \
|
|
|
166 Licensed under the Apache License 2.0\nhttp://www.apache.org/licenses/LICENSE-2.0"
|
|
|
167
|
|
|
168 if argv is None:
|
|
|
169 argv = sys.argv[1:]
|
|
|
170 try:
|
|
|
171 # setup option parser
|
|
|
172 parser = OptionParser(version=program_version_string, epilog=program_longdesc, description=program_license)
|
|
|
173 parser.add_option("-g", "--geno", dest="genofile", help="set input genotype file path [default: %default]", metavar="FILE")
|
|
|
174 parser.add_option("-s", "--sample", dest="samplefile", help="set input sample file path [default: %default]", metavar="FILE")
|
|
|
175 parser.add_option("-m", "--mapfile", dest="mapfile", help="set input map file path [default: %default]", metavar="FILE")
|
|
|
176 parser.add_option("-q", "--qtlfile", dest="qtlfile", help="set input QTL file path [default: %default]", metavar="FILE")
|
|
|
177 parser.add_option("-j", "--jar", dest="jarfile", help="set Flapjack project creator jar file path [default: %default]", metavar="FILE")
|
|
|
178 parser.add_option("-J", "--headerjar", dest="headerjar", help="set Flapjack header creator jar file path [default: %default]", metavar="FILE")
|
|
|
179 parser.add_option("-S", "--separator", dest="separator", help="declare separator for genotypes, '' for no separator [default: %default]")
|
|
|
180 parser.add_option("-M", "--missingGenotype", dest="missing", help="set missing genotype string [default: %default]")
|
|
|
181 parser.add_option("-v", "--verbose", dest="verbose", action="count", help="set verbosity level [default: %default]")
|
|
|
182
|
|
|
183 # process options
|
|
|
184 (opts, args) = parser.parse_args(argv)
|
|
|
185
|
|
|
186 if opts.verbose > 0:
|
|
|
187 print("verbosity level = %d" % opts.verbose)
|
|
|
188 if opts.genofile:
|
|
|
189 print("genofile = %s" % opts.genofile)
|
|
|
190 else:
|
|
|
191 sys.stderr.write("no genotype file detected!")
|
|
|
192 if opts.samplefile:
|
|
|
193 print("samplefile = %s" % opts.samplefile)
|
|
|
194 else:
|
|
|
195 sys.stderr.write("no sample file detected!")
|
|
|
196 if opts.mapfile:
|
|
|
197 print("mapfile = %s" % opts.mapfile)
|
|
|
198 else:
|
|
|
199 sys.stderr.write("no map file detected!")
|
|
|
200 if opts.qtlfile:
|
|
|
201 print("qtlfile = %s" % opts.qtlfile)
|
|
|
202 else:
|
|
|
203 sys.stderr.write("no QTL file detected!")
|
|
|
204 if opts.jarfile:
|
|
|
205 print("jarfile = %s" % opts.jarfile)
|
|
|
206 else:
|
|
|
207 sys.stderr.write("no Flapjack project creator jar file detected!")
|
|
|
208 if opts.headerjar:
|
|
|
209 print("headerjar = %s" % opts.headerjar)
|
|
|
210 else:
|
|
|
211 sys.stderr.write("no Flapjack header creator jar file detected!")
|
|
|
212
|
|
|
213 # MAIN BODY #
|
|
|
214 splitData(samplefile=opts.samplefile, genofile=opts.genofile)
|
|
|
215 createHeader(groups=parents, samplefile=opts.samplefile, genofile=opts.genofile, headerjar=opts.headerjar)
|
|
|
216 createProjectFile(groups=parents, samplefile=opts.samplefile, genofile=opts.genofile, jarfile=opts.jarfile, separator=opts.separator, missing=opts.missing,qtlfile=opts.qtlfile,mapfile=opts.mapfile)
|
|
|
217
|
|
|
218
|
|
|
219 except Exception, e:
|
|
|
220 indent = len(program_name) * " "
|
|
|
221 sys.stderr.write(program_name + ": " + repr(e) + "\n")
|
|
|
222 sys.stderr.write(indent + " for help use --help")
|
|
|
223 return 2
|
|
|
224
|
|
|
225
|
|
|
226 if __name__ == "__main__":
|
|
|
227 # if DEBUG:
|
|
|
228 # sys.argv.append("-h")
|
|
|
229 if TESTRUN:
|
|
|
230 import doctest
|
|
|
231 doctest.testmod()
|
|
|
232 if PROFILE:
|
|
|
233 import cProfile
|
|
|
234 import pstats
|
|
|
235 profile_filename = 'DNASampleSplitter_profile.txt'
|
|
|
236 cProfile.run('main()', profile_filename)
|
|
|
237 statsfile = open("profile_stats.txt", "wb")
|
|
|
238 p = pstats.Stats(profile_filename, stream=statsfile)
|
|
|
239 stats = p.strip_dirs().sort_stats('cumulative')
|
|
|
240 stats.print_stats()
|
|
|
241 statsfile.close()
|
|
|
242 sys.exit(0)
|
|
|
243 sys.exit(main()) |
