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