Mercurial > repos > cmonjeau > stacks
comparison STACKS_prepare_population_map.py @ 0:d6ba40f6c824
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author | cmonjeau |
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date | Mon, 24 Aug 2015 09:29:12 +0000 |
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-1:000000000000 | 0:d6ba40f6c824 |
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1 #!/usr/bin/env python | |
2 | |
3 import sys, re | |
4 import os | |
5 import tempfile | |
6 import shutil, subprocess, glob | |
7 import optparse | |
8 from os.path import basename | |
9 import zipfile, tarfile, gzip | |
10 from galaxy.datatypes.checkers import * | |
11 from stacks import * | |
12 | |
13 """ | |
14 | |
15 Created by Cyril Monjeaud | |
16 Cyril.Monjeaud@irisa.fr | |
17 | |
18 Last modifications : 01/10/2014 | |
19 | |
20 WARNING : | |
21 | |
22 STACKS_denovomap.py needs: | |
23 | |
24 - STACKS scripts in your $PATH | |
25 | |
26 These scripts are available after compiling the sources of STACKS : | |
27 | |
28 http://creskolab.uoregon.edu/stacks/ | |
29 | |
30 or with the galaxy_stacks package in the Genouest toolshed (http://toolshed.genouest.org) | |
31 | |
32 """ | |
33 def __main__(): | |
34 | |
35 # arguments recuperation | |
36 parser = optparse.OptionParser() | |
37 parser.add_option("-f") | |
38 parser.add_option("-s") | |
39 parser.add_option("-t") | |
40 parser.add_option("-o") | |
41 parser.add_option("-d") | |
42 (options, args) = parser.parse_args() | |
43 | |
44 # create the working dir | |
45 tmp_dir = tempfile.mkdtemp(dir=options.d) | |
46 | |
47 print tmp_dir | |
48 #os.chdir(tmp_dir) | |
49 | |
50 # parse config files | |
51 tab_fq_files=galaxy_config_to_tabfiles_for_STACKS(options.f) | |
52 | |
53 # check if zipped files are into the tab and change tab content | |
54 extract_compress_files_from_tabfiles(tab_fq_files, tmp_dir) | |
55 | |
56 # generate population map for denovo map | |
57 if not options.s: | |
58 generate_popmap_for_denovo(tab_fq_files, options.t, options.o) | |
59 else: | |
60 # parse config files | |
61 tab_sam_files=galaxy_config_to_tabfiles_for_STACKS(options.s) | |
62 extract_compress_files_from_tabfiles(tab_sam_files, tmp_dir) | |
63 generate_popmap_for_refmap(tab_fq_files, tab_sam_files, options.t, options.o) | |
64 | |
65 | |
66 #clean up temp files | |
67 shutil.rmtree( tmp_dir ) | |
68 | |
69 | |
70 | |
71 | |
72 | |
73 | |
74 if __name__ == "__main__": __main__() |