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1 # macs2 python wrapper
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2 # based on http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
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3
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4 import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
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5 from galaxy import eggs
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6 import json
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7
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8 CHUNK_SIZE = 1024
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9
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10 #==========================================================================================
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11 #functions
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12 #==========================================================================================
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13 def gunzip_cat_glob_path( glob_path, target_filename, delete = False ):
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14 out = open( target_filename, 'wb' )
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15 for filename in glob.glob( glob_path ):
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16 fh = gzip.open( filename, 'rb' )
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17 while True:
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18 data = fh.read( CHUNK_SIZE )
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19 if data:
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20 out.write( data )
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21 else:
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22 break
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23 fh.close()
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24 if delete:
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25 os.unlink( filename )
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26 out.close()
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27
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28 def xls_to_interval( xls_file, interval_file, header = None ):
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29 out = open( interval_file, 'wb' )
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30 if header:
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31 out.write( '#%s\n' % header )
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32 wrote_header = False
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33 #From macs readme: Coordinates in XLS is 1-based which is different with BED format.
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34 for line in open( xls_file ):
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35 #keep all existing comment lines
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36 if line.startswith( '#' ):
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37 out.write( line )
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38 #added for macs2 since there is an extra newline
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39 elif line.startswith( '\n' ):
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40 out.write( line )
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41 elif not wrote_header:
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42 out.write( '#%s' % line )
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43 print line
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44 wrote_header = True
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45 else:
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46 fields = line.split( '\t' )
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47 if len( fields ) > 1:
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48 fields[1] = str( int( fields[1] ) - 1 )
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49 out.write( '\t'.join( fields ) )
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50 out.close()
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51
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52 #==========================================================================================
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53 #main
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54 #==========================================================================================
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55 def main():
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56 #take in options file and output file names
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57 options = json.load( open( sys.argv[1] ) )
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58 outputs = json.load( open( sys.argv[2] ) )
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59
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60 #=================================================================================
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61 #parse options and execute macs2
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62 #=================================================================================
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63 #default inputs that are in every major command
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64 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for some file names
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65 cmdline = "macs2 %s -t %s" % ( options['command'], ",".join( options['input_chipseq'] ) )
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66 if options['input_control']:
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67 cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
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68
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69 #=================================================================================
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70 if (options['command'] == "callpeak"):
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71 output_bed = outputs['output_bed_file']
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72 output_extra_html = outputs['output_extra_file']
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73 output_extra_path = outputs['output_extra_file_path']
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74 output_peaks = outputs['output_peaks_file']
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75 output_narrowpeaks = outputs['output_narrowpeaks_file']
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76 output_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file']
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77 output_xls_to_interval_negative_peaks_file = outputs['output_xls_to_interval_negative_peaks_file']
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78
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79 if 'pvalue' in options:
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80 cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --pvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['pvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] )
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81 elif 'qvalue' in options:
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82 cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --qvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['qvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] )
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83
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84 if 'broad_cutoff' in options:
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85 cmdline += " --broad --broad-cutoff=%s" % (options['broad_cutoff'])
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86
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87 if 'nomodel' in options:
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88 cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] )
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89 #=================================================================================
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90 if (options['command'] == "bdgcmp"):
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91 output_bdgcmp = outputs['output_bdgcmp_file']
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92
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93 cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] )
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94 #=================================================================================
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95
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96 tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user
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97 stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report
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98 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
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99 proc.wait()
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100 #We don't want to set tool run to error state if only warnings or info, e.g. mfold could be decreased to improve model, but let user view macs log
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101 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
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102 if proc.returncode:
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103 stderr_f = open( stderr_name )
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104 while True:
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105 chunk = stderr_f.read( CHUNK_SIZE )
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106 if not chunk:
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107 stderr_f.close()
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108 break
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109 sys.stderr.write( chunk )
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110
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111 #=================================================================================
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112 #copy files created by macs2 to appripriate directory with the provided names
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113 #=================================================================================
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114
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115 #=================================================================================
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116 #move files generated by callpeak command
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117 if (options['command'] == "callpeak"):
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118 #run R to create pdf from model script
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119 if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ):
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120 cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name )
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121 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
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122 proc.wait()
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123
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124 #move bed out to proper output file
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125 created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name )
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126 if os.path.exists( created_bed_name ):
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127 shutil.move( created_bed_name, output_bed )
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128
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129 #OICR peak_xls file
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130 created_peak_xls_file = os.path.join( tmp_dir, "%s_peaks.xls" % experiment_name )
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131 if os.path.exists( created_peak_xls_file ):
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132 # shutil.copy( created_peak_xls_file, os.path.join ( "/mnt/galaxyData/tmp/", "%s_peaks.xls" % ( os.path.basename(output_extra_path) )))
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133 shutil.copyfile( created_peak_xls_file, output_peaks )
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134
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135 #peaks.encodepeaks (narrowpeaks) file
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136 created_narrowpeak_file = os.path.join (tmp_dir, "%s_peaks.encodePeak" % experiment_name )
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137 if os.path.exists( created_narrowpeak_file ):
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138 shutil.move (created_narrowpeak_file, output_narrowpeaks )
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139
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140 #parse xls files to interval files as needed
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141 #if 'xls_to_interval' in options:
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142 if (options['xls_to_interval'] == "True"):
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143 create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name )
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144 if os.path.exists( create_peak_xls_file ):
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145 xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' )
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146 create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name )
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147 if os.path.exists( create_peak_xls_file ):
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148 print "negative file exists"
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149 xls_to_interval( create_peak_xls_file, output_xls_to_interval_negative_peaks_file, header = 'negative peaks file' )
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150
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151 #move all remaining files to extra files path of html file output to allow user download
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152 out_html = open( output_extra_html, 'wb' )
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153 out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name )
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154 os.mkdir( output_extra_path )
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155 for filename in sorted( os.listdir( tmp_dir ) ):
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156 shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) )
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157 out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) )
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158 #out_html.write( '<li><a href="%s">%s</a>peakxls %s SomethingDifferent tmp_dir %s path %s exp_name %s</li>\n' % ( created_peak_xls_file, filename, filename, tmp_dir, output_extra_path, experiment_name ) )
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159 out_html.write( '</ul></p>\n' )
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160 out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() )
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161 out_html.write( '</body></html>\n' )
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162 out_html.close()
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163
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164 #=================================================================================
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165 #move files generated by bdgcmp command
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166 if (options['command'] == "bdgcmp"):
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167 created_bdgcmp_file = os.path.join (tmp_dir, "bdgcmp_out.bdg" )
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168 if os.path.exists( created_bdgcmp_file ):
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169 shutil.move (created_bdgcmp_file, output_bdgcmp )
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170
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171 #=================================================================================
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172 #cleanup
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173 #=================================================================================
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174 os.unlink( stderr_name )
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175 os.rmdir( tmp_dir )
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176
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177 if __name__ == "__main__": main()
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