comparison STACKS_prepare_population_map.py @ 0:d6ba40f6c824

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author cmonjeau
date Mon, 24 Aug 2015 09:29:12 +0000
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-1:000000000000 0:d6ba40f6c824
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__()