Mercurial > repos > modencode-dcc > peakranger

comparison ranger_wrapper.py @ 17:d2319b4df472 draft

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author modencode-dcc
date Mon, 21 Jan 2013 14:00:26 -0500
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16:5b356acc1a4a 17:d2319b4df472
1 #purpose: python wrapper to run peak ranger
2 #author: Ziru Zhou
3 #Date: November 2012
4
5 import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
6 from galaxy import eggs
7 import pkg_resources
8 pkg_resources.require( "simplejson" )
9 import simplejson
10 import glob
11 import datetime
12
13 CHUNK_SIZE = 1024
14
15 def main():
16 options = simplejson.load( open( sys.argv[1] ) )
17 outputs = simplejson.load( open( sys.argv[2] ) )
18 script_path = sys.argv[3]
19
20
21 #sets experiment name and sets the chip/input files
22 #========================================================================================
23 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name
24
25 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/peakranger %s -d %s --format bam" % ( options['action'], options['chip_file'] )
26 cmdline = "peakranger %s -d %s" % ( options['action'], options['chip_file'] )
27 if 'input_file' in options:
28 cmdline = "%s -c %s" % ( cmdline, options['input_file'] )
29
30 #set additional options
31 #========================================================================================
32 if (options['action'] == "nr"):
33 output_ranger_file = outputs['output_ranger_file']
34
35 cmdline = "%s --format bam -l %s --verbose > default_output.txt" % ( cmdline, options['extension'] )
36 elif (options['action'] == "lc"):
37 output_ranger_file = outputs['output_ranger_file']
38
39 cmdline = "%s --verbose > default_output.txt" % ( cmdline )
40 elif (options['action'] == "wig"):
41 output_wigzip_file = outputs['output_wigzip_file']
42
43 cmdline = "%s --format bam -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] )
44 elif (options['action'] == "wigpe"):
45 output_wigzip_file = outputs['output_wigzip_file']
46
47 cmdline = "%s -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] )
48 elif (options['action'] == "ranger"):
49 output_summit_file = outputs['output_summit_file']
50 output_region_file = outputs['output_region_file']
51 output_details_file = outputs['output_details_file']
52 output_report_file = outputs['output_report_file']
53
54 if (options['gene_annotate_file'] != "None"):
55 gene_annotate_file = "--gene_annot_file %s/gene_annotation_files/%s" % ( script_path, options['gene_annotate_file'] )
56 report = "--report"
57 elif (options['gene_annotate_file'] == "Upload"):
58 gene_annotate_file = options['usr_annot_file']
59 report = "--report"
60 else:
61 gene_annotate_file = ""
62 report = ""
63
64 cmdline = "%s -t %s --format bam %s --plot_region %s -l %s -p %s -q %s -r %s -b %s %s %s -o ranger_peak" % ( cmdline, options['threads'], gene_annotate_file, options['plot_region'], options['extension'], options['pvalue'], options['fdr'], options['delta'], options['bandwith'], options['pad'], report )
65 elif (options['action'] == "ccat"):
66 output_summit_file = outputs['output_summit_file']
67 output_region_file = outputs['output_region_file']
68 output_details_file = outputs['output_details_file']
69 output_report_file = outputs['output_report_file']
70 output_ranger_file = outputs['output_ranger_file']
71
72 if (options['gene_annotate_file'] != "None"):
73 gene_annotate_file = "--gene_annot_file %s/gene_annotation_files/%s" % ( script_path, options['gene_annotate_file'] )
74 report = "--report"
75 elif (options['gene_annotate_file'] == "Upload"):
76 gene_annotate_file = options['usr_annot_file']
77 report = "--report"
78 else:
79 gene_annotate_file = ""
80 report = ""
81
82 cmdline = "%s --format bam %s --plot_region %s -l %s -q %s --win_size %s --win_step %s --min_count %s --min_score %s %s -o ranger_peak > default_output.txt" % ( cmdline, gene_annotate_file, options['plot_region'], options['extension'], options['fdr'], options['winsize'], options['winstep'], options['mincount'], options['minscore'], report )
83
84 #run cmdline
85 #========================================================================================
86 tmp_dir = tempfile.mkdtemp()
87 stderr_name = tempfile.NamedTemporaryFile().name
88 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
89 proc.wait()
90
91 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
92 #========================================================================================
93 if proc.returncode:
94 stderr_f = open( stderr_name )
95 while True:
96 chunk = stderr_f.read( CHUNK_SIZE )
97 if not chunk:
98 stderr_f.close()
99 break
100 sys.stderr.write( chunk )
101
102
103 #determine if the outputs are there, copy them to the appropriate dir and filename
104 #========================================================================================
105 if(options['action'] == "nr" or options['action'] == "lc" or options['action'] == "ccat"):
106 created_ranger_file = os.path.join( tmp_dir, "default_output.txt" )
107 if os.path.exists( created_ranger_file ):
108 shutil.move( created_ranger_file, output_ranger_file )
109
110 if(options['action'] == "wig" or options['action'] == "wigpe"):
111 if(options['split'] == "-s" or options['strand'] == "-x"):
112 if(options['gzip'] == "-z"):
113 files = str( glob.glob('%s/*.wig.gz' % tmp_dir) )
114 files = files.replace("[", "")
115 files = files.replace("]", "")
116 files = files.replace(",", "")
117 files = files.replace("'", "")
118 cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
119 #cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
120 os.system(cmd)
121 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )
122 else:
123 files = str( glob.glob('%s/*.wig' % tmp_dir) )
124 files = files.replace("[", "")
125 files = files.replace("]", "")
126 files = files.replace(",", "")
127 files = files.replace("'", "")
128 cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
129 #cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
130 os.system(cmd)
131 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )
132 else:
133 if(options['gzip'] == "-z"):
134 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig.gz" )
135 else:
136 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig" )
137
138 if os.path.exists( created_wigzip_file ):
139 shutil.move( created_wigzip_file, output_wigzip_file )
140
141 if(options['action'] == "ranger" or options['action'] == "ccat"):
142 created_summit_file = os.path.join( tmp_dir, "ranger_peak_summit.bed" )
143 if os.path.exists( created_summit_file ):
144 shutil.move( created_summit_file, output_summit_file )
145
146 created_region_file = os.path.join( tmp_dir, "ranger_peak_region.bed" )
147 if os.path.exists( created_region_file ):
148 shutil.move( created_region_file, output_region_file )
149
150 created_details_file = os.path.join( tmp_dir, "ranger_peak_details" )
151 if os.path.exists( created_details_file ):
152 shutil.move( created_details_file, output_details_file )
153
154 #zips the html report and puts it in history, whole report is too big and display in galaxy is very unformatted
155 filename = os.path.splitext(os.path.basename(options['chip_file']))[0]
156 filename = filename.upper()
157 extension = os.path.splitext(options['chip_file'])[1]
158 extension = extension.replace(".", "")
159 extension = extension.upper()
160 now = datetime.datetime.now()
161 date = now.strftime("%Y-%m-%d")
162 foldername = "%s_%s_REPORT_%s" % (filename, extension, date)
163
164 created_report_file = os.path.join( tmp_dir, foldername )
165 if os.path.exists ( created_report_file ):
166 #os.system("cp -rf %s %s" % (created_report_file, "/mnt/galaxyData/files/000/"))
167 os.system("cp -rf %s ." % created_report_file)
168 os.system("zip -r created_report.zip %s > /dev/null" % foldername)
169 #os.system("zip -r created_report.zip /mnt/galaxyData/files/000/%s > /dev/null" % foldername)
170 shutil.move( "created_report.zip", output_report_file)
171
172
173 #os.system("ln -fs %s/index.html %s" %( foldername, output_report_file ))
174 #datafoldername = os.path.splitext(os.path.basename(output_report_file))
175 #datafolder = os.path.join ("/mnt/galaxyData/files/000/" datafoldername)
176 #print "datafolder %s" % datafolder
177 #if os.path.exists( datafolder )
178 # os.system("rm -rf %s" % datafolder)
179 # os.system("cp -rf %s/%s/imgs /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
180 # os.system("cp -rf %s/%s/scripts /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
181
182 os.unlink( stderr_name )
183 shutil.rmtree( tmp_dir )
184
185 if __name__ == "__main__": main()