Mercurial > repos > cmonjeau > stacks

comparison STACKS_procrad.py @ 0:d6ba40f6c824

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first commit
author cmonjeau
date Mon, 24 Aug 2015 09:29:12 +0000
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children c9e10e0d6c10
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-1:000000000000 0:d6ba40f6c824
1 #!/usr/bin/python
2 # -*- coding: utf-8 -*-
3
4 import sys
5 import os
6 import re
7 import tempfile
8 import subprocess
9 import glob
10 import shutil
11 import argparse
12 from os.path import basename
13 import zipfile
14 import tarfile
15 import gzip
16 from stacks import *
17
18
19 def __main__():
20
21 # arguments recuperation
22
23 parser = argparse.ArgumentParser()
24 parser.add_argument('--input_type')
25 parser.add_argument('--input_enzyme')
26 parser.add_argument('--input_single')
27 parser.add_argument('--input_paired1')
28 parser.add_argument('--input_paired2')
29 parser.add_argument('--inputype')
30 parser.add_argument('--sample_name')
31 parser.add_argument('--barcode')
32 parser.add_argument('--output_choice')
33 parser.add_argument('--output_archive')
34 parser.add_argument('--enzyme1')
35 parser.add_argument('--enzyme2')
36 parser.add_argument('--outype')
37 parser.add_argument('--qualitenc')
38 parser.add_argument('-D', action='store_true')
39 parser.add_argument('-t')
40 parser.add_argument('-q', action='store_true')
41 parser.add_argument('--activate_advanced_options')
42 parser.add_argument('-r', action='store_true')
43 parser.add_argument('-w', default='0.15')
44 parser.add_argument('-s', default='10')
45 parser.add_argument('-c', action='store_true')
46 parser.add_argument('--inline_null', action='store_true')
47 parser.add_argument('--index_null', action='store_true')
48 parser.add_argument('--inline_inline', action='store_true')
49 parser.add_argument('--index_index', action='store_true')
50 parser.add_argument('--inline_index', action='store_true')
51 parser.add_argument('--index_inline', action='store_true')
52 parser.add_argument('--logfile')
53 options = parser.parse_args()
54
55 # create the working dir
56 os.mkdir('inputs')
57 os.mkdir('job_outputs')
58 os.mkdir('galaxy_outputs')
59
60 cmd_line = []
61 cmd_line.append('process_radtags')
62 cmd_line.extend(['-p', 'inputs'])
63 cmd_line.extend(['-i', options.inputype])
64 cmd_line.extend(['-b', options.barcode])
65
66 # parse config files and create symlink into the temp dir
67
68 if options.input_type == 'single':
69
70 # load the config file
71 input_single = options.input_single
72
73 # parse the input_file to extract filenames and filepaths
74 tab_files = galaxy_config_to_tabfiles(input_single)
75
76 # create symlink into the temp dir
77 create_symlinks_from_tabfiles(tab_files, 'inputs')
78 else:
79
80 # load config files
81 input_paired1 = options.input_paired1
82 input_paired2 = options.input_paired2
83
84 # parse the input_file to extract filenames and filepaths
85
86 tab_files_paired1 = galaxy_config_to_tabfiles(input_paired1)
87 tab_files_paired2 = galaxy_config_to_tabfiles(input_paired2)
88
89 # create symlinks into the temp dir
90
91 create_symlinks_from_tabfiles(tab_files_paired1, 'inputs')
92 create_symlinks_from_tabfiles(tab_files_paired2, 'inputs')
93
94 cmd_line.append('-P')
95
96 # test nb enzyme
97 if options.input_enzyme == '1':
98 cmd_line.extend(['-e', options.enzyme1])
99
100 if options.input_enzyme == '2':
101 cmd_line.extend(['---renz_1', options.enzyme1, '--renz_2', options.enzyme2])
102
103 # quality
104 cmd_line.extend(['-E', options.qualitenc])
105
106 # outputs
107 cmd_line.extend(['-o', 'job_outputs/'])
108 cmd_line.extend(['-y', options.outype])
109
110 # test capture discards
111 if options.D:
112 cmd_line.append('-D')
113
114 # optional options
115 if options.activate_advanced_options == "true":
116
117 if options.q:
118 cmd_line.append('-q')
119 if options.r:
120 cmd_line.append('-r')
121
122 cmd_line.extend(['-w', options.w, '-s', options.s])
123
124 if options.c:
125 cmd_line.append('-c')
126 if options.t != '-1':
127 cmd_line.extend(['-t', options.t])
128 if options.inline_null:
129 cmd_line.append('--inline_null')
130 if options.index_null:
131 cmd_line.append('--index_null')
132 if options.inline_inline:
133 cmd_line.append('--inline_inline')
134 if options.index_index:
135 cmd_line.append('--index_index')
136 if options.inline_index:
137 cmd_line.append('--inline_index')
138 if options.index_inline:
139 cmd_line.append('--index_inline')
140
141 print '[CMD_LINE] : ' + ' '.join(cmd_line)
142
143 p = subprocess.call(cmd_line)
144
145 # postprocesses
146
147 try:
148 shutil.move('job_outputs/process_radtags.log', options.logfile)
149 except:
150 sys.stderr.write('Error in process_radtags execution; Please read the additional output (stdout)\n')
151 sys.exit(1)
152
153 if options.discard_file:
154 discards_file_name = glob.glob('job_outputs/*.discards')[0]
155 shutil.move(discards_file_name, options.discard_file)
156
157 # manage outputs names
158
159 change_outputs_procrad_name(os.getcwd() + '/job_outputs', options.sample_name)
160
161 # generate additional output archive file
162
163 if options.output_choice != '1':
164 generate_additional_archive_file(os.getcwd() + '/job_outputs', options.output_archive)
165
166 # if user has not choose the only zip archive
167
168 if options.output_choice != '3':
169 list_files = glob.glob('job_outputs/*')
170 for i in list_files:
171 shutil.move(i, 'galaxy_outputs')
172
173
174 if __name__ == '__main__':
175 __main__()
176
177