Mercurial > repos > weilong-guo > bs_seeker2

comparison BSseeker2/galaxy/bs_seeker2_wrapper.py @ 0:e6df770c0e58 draft

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Initial upload
author weilong-guo
date Fri, 12 Jul 2013 18:47:28 -0400
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children 8b26adf64adc
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-1:000000000000 0:e6df770c0e58
1 import tempfile
2
3 __author__ = 'pf'
4 from subprocess import Popen
5 from collections import defaultdict
6 import sys, shutil, os, re
7
8
9
10 BUILD = 'build'
11 ALIGN = 'align'
12 CALL_METHYLATION = 'call_methylation'
13
14 EXEC = 'exec'
15 EXEC_PATH = EXEC+'-path'
16 ARG_TYPES = [BUILD, ALIGN, CALL_METHYLATION, EXEC]
17
18 USAGE = """
19 %(script)s is a wrapper script for bs_seeker2-build.py and bs_seeker2-align.py that is intended to be used with the Galaxy web platform.
20 The script takes command line parameters and runs bs_seeker2-align.py and bs_seeker2-build.py, if neccessary.
21
22 The parameters that are related to bs_seeker2-build.py must be prefixed with --%(build_tag)s.
23 The parameters that are related to bs_seeker2-align.py must be prefixed with --%(align_tag)s.
24 Additionally, the path to BS-Seeker2 has to be specified via the --%(exec_path)s option.
25
26 For example:
27
28 python %(script)s --%(exec_path)s /mnt/Data/UCLA/Matteo/BS-Seeker --build-f data/arabidopsis/genome/Arabidopsis.fa --align-i data/arabidopsis/BS6_N1try2L7_seq.txt.fa --align-o data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output
29
30 This will run build the genome in Arabidopsis.fa and put the indexes in a temporary directory. bs_seeker2-align.py will be run on the
31 newly created genome index. I.e. the following two commands will be run in a shell:
32
33 python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-build.py --db /tmp/tmpg8Eq1o -f /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/genome/Arabidopsis.fa
34
35 python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-align.py --db /tmp/tmpg8Eq1o -o /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output -i /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa -g Arabidopsis.fa
36
37
38 The temporary directory will be deleted after the wrapper exits.
39
40
41 If no options related to bs_seeker2-build are passed, no genome index will be built and the corresponding pre-built genome index will be used
42 instead. No temporary files and directories will be created.
43
44 """ % { 'script' : os.path.split(__file__)[1], 'build_tag' :BUILD, 'align_tag' : ALIGN, 'exec_path' : EXEC_PATH }
45
46
47 def error(msg):
48 print >> sys.stderr, 'ERROR: %s' % msg
49 exit(1)
50
51
52 if __name__ == '__main__':
53 if len(sys.argv) == 1:
54 error('No parameters\n\n'+USAGE)
55
56
57 # Parse command line arguments
58 args = defaultdict(dict)
59 arg_key = None
60 arg_val = None
61 arg_type = None
62
63 for arg in sys.argv[1:]:
64 if arg.startswith('--'):
65 try:
66 arg_type, arg_key = re.match(r'--(\w+)(.*)', arg).groups()
67 if arg_type not in ARG_TYPES:
68 raise Exception("Bad argument: %s. arg_type (%s) must be one of: %s." % (arg, arg_type, ', '.join(ARG_TYPES)))
69 if not arg_key or arg_key[0] != '-':
70 raise Exception("Bad argument: %s. arg_key (%s) must start with - or --." % (arg, arg_key))
71 except Exception, e:
72 error(str(e) + '\n\n' + USAGE)
73 args[arg_type][arg_key] = ''
74 else:
75 args[arg_type][arg_key] = arg
76
77 path_to_bs_seeker = args.get('exec', {'-path' : None})['-path'] # return None when exec not found
78 if path_to_bs_seeker is None:
79 error('You have to specify the path to BS-Seeker2 via --%s\n\n' % EXEC_PATH + USAGE)
80
81 tempdir = None
82 def run_prog(prog, params):
83 cwd, _ = os.path.split(__file__)
84 cmd = 'python %(prog)s %(params)s' % {
85 'prog' : os.path.join(cwd, prog),
86 'params' : ' '.join('%s %s' % (arg_key, arg_val) for arg_key, arg_val in params.items())
87 }
88 print 'exec:', cmd
89
90 return_code = Popen(args = cmd, shell = True).wait()
91 if return_code:
92 if tempdir:
93 shutil.rmtree(tempdir)
94 error("%s exit with error code %d" % (prog, return_code))
95 tempdir = tempfile.mkdtemp()
96
97 # bs_seeker2-build
98 if BUILD in args:
99 args[BUILD]['--db'] = tempdir
100 args[ALIGN]['--db'] = tempdir
101 run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-build.py'), args[BUILD])
102
103 # bs_seeker2-align
104 args[ALIGN]['--temp_dir'] = tempdir
105 run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-align.py'), args[ALIGN])
106
107
108 def getopt(h, k1, k2, default):
109 return h.get(k1, h.get(k2, default))
110 # bs_seeker2-call_methylation
111 args[CALL_METHYLATION].update({ '-i' : args[ALIGN]['--output'],
112 '--db' : os.path.join(args[ALIGN]['--db'],
113 os.path.split( getopt(args[ALIGN],'-g', '--genome', None))[1] +
114 ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'),
115 getopt(args[ALIGN], '-u', '--up', '500'))
116 if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') +
117
118 '_' + args[ALIGN]['--aligner'])
119 })
120 run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION])
121
122 if tempdir:
123 shutil.rmtree(tempdir)