comparison ranger_wrapper.py @ 5:a8e81a2e6bf8 draft

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author modencode-dcc
date Thu, 17 Jan 2013 16:18:25 -0500
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4:49542dea5b60 5:a8e81a2e6bf8
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
19
20 #sets experiment name and sets the chip/input files
21 #========================================================================================
22 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name
23
24 #cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/peakranger %s -d %s --format bam" % ( options['action'], options['chip_file'] )
25 cmdline = "peakranger %s -d %s" % ( options['action'], options['chip_file'] )
26 if 'input_file' in options:
27 cmdline = "%s -c %s" % ( cmdline, options['input_file'] )
28
29 #set additional options
30 #========================================================================================
31 if (options['action'] == "nr"):
32 output_ranger_file = outputs['output_ranger_file']
33
34 cmdline = "%s --format bam -l %s --verbose > default_output.txt" % ( cmdline, options['extension'] )
35 elif (options['action'] == "lc"):
36 output_ranger_file = outputs['output_ranger_file']
37
38 cmdline = "%s --verbose > default_output.txt" % ( cmdline )
39 elif (options['action'] == "wig"):
40 output_wigzip_file = outputs['output_wigzip_file']
41
42 cmdline = "%s --format bam -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] )
43 elif (options['action'] == "wigpe"):
44 output_wigzip_file = outputs['output_wigzip_file']
45
46 cmdline = "%s -l %s %s %s %s -o ranger_wig" % ( cmdline, options['extension'], options['split'], options['strand'], options['gzip'] )
47 elif (options['action'] == "ranger"):
48 output_summit_file = outputs['output_summit_file']
49 output_region_file = outputs['output_region_file']
50 output_details_file = outputs['output_details_file']
51 output_report_file = outputs['output_report_file']
52
53 if (options['gene_annotate_file'] != "None"):
54 gene_annotate_file = "--gene_annot_file /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/gene_annotation_files/%s" % options['gene_annotate_file']
55 report = "--report"
56 elif (options['gene_annotate_file'] == "Upload"):
57 gene_annotate_file = options['usr_annot_file']
58 report = "--report"
59 else:
60 gene_annotate_file = ""
61 report = ""
62
63 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 )
64 elif (options['action'] == "ccat"):
65 output_summit_file = outputs['output_summit_file']
66 output_region_file = outputs['output_region_file']
67 output_details_file = outputs['output_details_file']
68 output_report_file = outputs['output_report_file']
69 output_ranger_file = outputs['output_ranger_file']
70
71 if (options['gene_annotate_file'] != "None"):
72 gene_annotate_file = "--gene_annot_file /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/peakranger/gene_annotation_files/%s" % options['gene_annotate_file']
73 report = "--report"
74 elif (options['gene_annotate_file'] == "Upload"):
75 gene_annotate_file = options['usr_annot_file']
76 report = "--report"
77 else:
78 gene_annotate_file = ""
79 report = ""
80
81 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 )
82
83 #run cmdline
84 #========================================================================================
85 tmp_dir = tempfile.mkdtemp()
86 stderr_name = tempfile.NamedTemporaryFile().name
87 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
88 proc.wait()
89
90 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
91 #========================================================================================
92 if proc.returncode:
93 stderr_f = open( stderr_name )
94 while True:
95 chunk = stderr_f.read( CHUNK_SIZE )
96 if not chunk:
97 stderr_f.close()
98 break
99 sys.stderr.write( chunk )
100
101
102 #determine if the outputs are there, copy them to the appropriate dir and filename
103 #========================================================================================
104 if(options['action'] == "nr" or options['action'] == "lc" or options['action'] == "ccat"):
105 created_ranger_file = os.path.join( tmp_dir, "default_output.txt" )
106 if os.path.exists( created_ranger_file ):
107 shutil.move( created_ranger_file, output_ranger_file )
108
109 if(options['action'] == "wig" or options['action'] == "wigpe"):
110 if(options['split'] == "-s" or options['strand'] == "-x"):
111 if(options['gzip'] == "-z"):
112 files = str( glob.glob('%s/*.wig.gz' % tmp_dir) )
113 files = files.replace("[", "")
114 files = files.replace("]", "")
115 files = files.replace(",", "")
116 files = files.replace("'", "")
117 cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
118 #cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
119 os.system(cmd)
120 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )
121 else:
122 files = str( glob.glob('%s/*.wig' % tmp_dir) )
123 files = files.replace("[", "")
124 files = files.replace("]", "")
125 files = files.replace(",", "")
126 files = files.replace("'", "")
127 cmd = "zip -j %s/ranger_wig.zip %s > /dev/null" % (tmp_dir, files)
128 #cmd = "tar -czvf %s/ranger_wig.tar %s > /dev/null" % (tmp_dir, files)
129 os.system(cmd)
130 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.zip" )
131 else:
132 if(options['gzip'] == "-z"):
133 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig.gz" )
134 else:
135 created_wigzip_file = os.path.join( tmp_dir, "ranger_wig.wig" )
136
137 if os.path.exists( created_wigzip_file ):
138 shutil.move( created_wigzip_file, output_wigzip_file )
139
140 if(options['action'] == "ranger" or options['action'] == "ccat"):
141 created_summit_file = os.path.join( tmp_dir, "ranger_peak_summit.bed" )
142 if os.path.exists( created_summit_file ):
143 shutil.move( created_summit_file, output_summit_file )
144
145 created_region_file = os.path.join( tmp_dir, "ranger_peak_region.bed" )
146 if os.path.exists( created_region_file ):
147 shutil.move( created_region_file, output_region_file )
148
149 created_details_file = os.path.join( tmp_dir, "ranger_peak_details" )
150 if os.path.exists( created_details_file ):
151 shutil.move( created_details_file, output_details_file )
152
153 #zips the html report and puts it in history, whole report is too big and display in galaxy is very unformatted
154 filename = os.path.splitext(os.path.basename(options['chip_file']))[0]
155 filename = filename.upper()
156 extension = os.path.splitext(options['chip_file'])[1]
157 extension = extension.replace(".", "")
158 extension = extension.upper()
159 now = datetime.datetime.now()
160 date = now.strftime("%Y-%m-%d")
161 foldername = "%s_%s_REPORT_%s" % (filename, extension, date)
162
163 created_report_file = os.path.join( tmp_dir, foldername )
164 if os.path.exists ( created_report_file ):
165 #os.system("cp -rf %s %s" % (created_report_file, "/mnt/galaxyData/files/000/"))
166 os.system("cp -rf %s ." % created_report_file)
167 os.system("zip -r created_report.zip %s > /dev/null" % foldername)
168 #os.system("zip -r created_report.zip /mnt/galaxyData/files/000/%s > /dev/null" % foldername)
169 shutil.move( "created_report.zip", output_report_file)
170
171
172 #os.system("ln -fs %s/index.html %s" %( foldername, output_report_file ))
173 #datafoldername = os.path.splitext(os.path.basename(output_report_file))
174 #datafolder = os.path.join ("/mnt/galaxyData/files/000/" datafoldername)
175 #print "datafolder %s" % datafolder
176 #if os.path.exists( datafolder )
177 # os.system("rm -rf %s" % datafolder)
178 # os.system("cp -rf %s/%s/imgs /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
179 # os.system("cp -rf %s/%s/scripts /mnt/galaxyData/files/000/%s" % (tmp_dir, foldername, datafolder))
180
181 os.unlink( stderr_name )
182 shutil.rmtree( tmp_dir )
183
184 if __name__ == "__main__": main()