Mercurial > repos > bgruening > bismark

comparison bismark_methylation_extractor.py @ 0:62c6da72dd4a draft

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author bgruening
date Sat, 06 Jul 2013 09:57:36 -0400
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children 91f07ff056ca
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-1:000000000000 0:62c6da72dd4a
1 #!/usr/bin/env python
2
3 import argparse, os, shutil, subprocess, sys, tempfile, fileinput
4 import zipfile
5 from glob import glob
6
7 def stop_err( msg ):
8 sys.stderr.write( "%s\n" % msg )
9 sys.exit()
10
11 def zipper(dir, zip_file):
12 zip = zipfile.ZipFile(zip_file, 'w', compression=zipfile.ZIP_DEFLATED)
13 root_len = len(os.path.abspath(dir))
14 for root, dirs, files in os.walk(dir):
15 archive_root = os.path.abspath(root)[root_len:]
16 for f in files:
17 fullpath = os.path.join(root, f)
18 archive_name = os.path.join(archive_root, f)
19 zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
20 zip.close()
21 return zip_file
22
23 def __main__():
24 #Parse Command Line
25 parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')
26
27 # input options
28 parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
29
30 parser.add_argument( '--infile', help='Input file in SAM format.' )
31 parser.add_argument( '--single-end', dest='single_end', action="store_true" )
32 parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )
33
34 parser.add_argument( '--report-file', dest='report_file' )
35 parser.add_argument( '--comprehensive', action="store_true" )
36 parser.add_argument( '--merge-non-cpg', dest='merge_non_cpg', action="store_true" )
37 parser.add_argument( '--no-overlap', dest='no_overlap', action="store_true" )
38 parser.add_argument( '--compress' )
39 parser.add_argument( '--ignore-bps', dest='ignore_bps', type=int )
40
41 # OT - original top strand
42 parser.add_argument( '--cpg_ot' )
43 parser.add_argument( '--chg_ot' )
44 parser.add_argument( '--chh_ot' )
45 # CTOT - complementary to original top strand
46 parser.add_argument( '--cpg_ctot' )
47 parser.add_argument( '--chg_ctot' )
48 parser.add_argument( '--chh_ctot' )
49 # OB - original bottom strand
50 parser.add_argument( '--cpg_ob' )
51 parser.add_argument( '--chg_ob' )
52 parser.add_argument( '--chh_ob' )
53 # CTOT - complementary to original bottom strand
54 parser.add_argument( '--cpg_ctob' )
55 parser.add_argument( '--chg_ctob' )
56 parser.add_argument( '--chh_ctob' )
57
58 parser.add_argument( '--cpg_context' )
59 parser.add_argument( '--chg_context' )
60 parser.add_argument( '--chh_context' )
61
62 parser.add_argument( '--non_cpg_context' )
63
64 parser.add_argument( '--non_cpg_context_ot' )
65 parser.add_argument( '--non_cpg_context_ctot' )
66 parser.add_argument( '--non_cpg_context_ob' )
67 parser.add_argument( '--non_cpg_context_ctob' )
68
69 args = parser.parse_args()
70
71
72 # Build methylation extractor command
73 output_dir = tempfile.mkdtemp()
74 cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'
75 if args.bismark_path:
76 # add the path to the bismark perl scripts, that is needed for galaxy
77 cmd = os.path.join(args.bismark_path, cmd)
78
79 additional_opts = ''
80 # Set up all options
81 if args.single_end:
82 additional_opts += ' --single-end '
83 else:
84 additional_opts += ' --paired-end '
85 if args.no_overlap:
86 additional_opts += ' --no_overlap '
87 if args.ignore_bps:
88 additional_opts += ' --ignore %s ' % args.ignore_bps
89 if args.comprehensive:
90 additional_opts += ' --comprehensive '
91 if args.merge_non_cpg:
92 additional_opts += ' --merge_non_CpG '
93 if args.report_file:
94 additional_opts += ' --report '
95
96
97 # Final command:
98 cmd = cmd % (output_dir, additional_opts, args.infile)
99
100 # Run
101 try:
102 tmp_out = tempfile.NamedTemporaryFile().name
103 tmp_stdout = open( tmp_out, 'wb' )
104 tmp_err = tempfile.NamedTemporaryFile().name
105 tmp_stderr = open( tmp_err, 'wb' )
106 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
107 returncode = proc.wait()
108 tmp_stderr.close()
109 # get stderr, allowing for case where it's very large
110 tmp_stderr = open( tmp_err, 'rb' )
111 stderr = ''
112 buffsize = 1048576
113 try:
114 while True:
115 stderr += tmp_stderr.read( buffsize )
116 if not stderr or len( stderr ) % buffsize != 0:
117 break
118 except OverflowError:
119 pass
120 tmp_stdout.close()
121 tmp_stderr.close()
122 if returncode != 0:
123 raise Exception, stderr
124
125 # TODO: look for errors in program output.
126 except Exception, e:
127 stop_err( 'Error in bismark methylation extractor:\n' + str( e ) )
128
129
130 # collect and copy output files
131
132 if args.compress:
133 zipper(output_dir, args.compress)
134
135
136 if args.cpg_ot:
137 shutil.move( glob(os.path.join( output_dir, '*CpG_OT_*'))[0], args.cpg_ot )
138 if args.chg_ot:
139 shutil.move( glob(os.path.join( output_dir, '*CHG_OT_*'))[0], args.chg_ot )
140 if args.chh_ot:
141 shutil.move( glob(os.path.join( output_dir, '*CHH_OT_*'))[0], args.chh_ot )
142 if args.cpg_ctot:
143 shutil.move( glob(os.path.join( output_dir, '*CpG_CTOT_*'))[0], args.cpg_ctot )
144 if args.chg_ctot:
145 shutil.move( glob(os.path.join( output_dir, '*CHG_CTOT_*'))[0], args.chg_ctot )
146 if args.chh_ctot:
147 shutil.move( glob(os.path.join( output_dir, '*CHH_CTOT_*'))[0], args.chh_ctot )
148 if args.cpg_ob:
149 shutil.move( glob(os.path.join( output_dir, '*CpG_OB_*'))[0], args.cpg_ob )
150 if args.chg_ob:
151 shutil.move( glob(os.path.join( output_dir, '*CHG_OB_*'))[0], args.chg_ob )
152 if args.chh_ob:
153 shutil.move( glob(os.path.join( output_dir, '*CHH_OB_*'))[0], args.chh_ob )
154 if args.cpg_ctob:
155 shutil.move( glob(os.path.join( output_dir, '*CpG_CTOB_*'))[0], args.cpg_ctob )
156 if args.chg_ctob:
157 shutil.move( glob(os.path.join( output_dir, '*CHG_CTOB_*'))[0], args.chg_ctob )
158 if args.chh_ctob:
159 shutil.move( glob(os.path.join( output_dir, '*CHH_CTOB_*'))[0], args.chh_ctob )
160
161 # context-dependent methylation output files
162 if args.cpg_context:
163 shutil.move( glob(os.path.join( output_dir, '*CpG_context_*'))[0], args.cpg_context )
164 if args.chg_context:
165 shutil.move( glob(os.path.join( output_dir, '*CHG_context_*'))[0], args.chg_context )
166 if args.chh_context:
167 shutil.move( glob(os.path.join( output_dir, '*CHH_context_*'))[0], args.chh_context )
168
169 if args.non_cpg_context:
170 shutil.move( glob(os.path.join( output_dir, '*Non_CpG_context_*'))[0], args.non_cpg_context )
171
172 if args.non_cpg_context_ot:
173 shutil.move( glob(os.path.join( output_dir, '*Non_CpG_OT_*'))[0], args.non_cpg_context_ot )
174 if args.non_cpg_context_ctot:
175 shutil.move( glob(os.path.join( output_dir, '*Non_CpG_CTOT_*'))[0], args.non_cpg_context_ctot )
176 if args.non_cpg_context_ob:
177 shutil.move( glob(os.path.join( output_dir, '*Non_CpG_OB_*'))[0], args.non_cpg_context_ob )
178 if args.non_cpg_context_ctob:
179 shutil.move( glob(os.path.join( output_dir, '*Non_CpG_CTOB_*'))[0], args.non_cpg_context_ctob )
180
181
182
183 if args.report_file:
184 shutil.move( glob(os.path.join( output_dir, '*_splitting_report*'))[0], args.report_file )
185
186
187 # Clean up temp dirs
188 if os.path.exists( output_dir ):
189 shutil.rmtree( output_dir )
190
191 if __name__=="__main__": __main__()