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1 #purpose: macs2 python wrapper
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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
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11 CHUNK_SIZE = 1024
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12
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13 #==========================================================================================
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14 #functions
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15 #==========================================================================================
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16 def gunzip_cat_glob_path( glob_path, target_filename, delete = False ):
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17 out = open( target_filename, 'wb' )
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18 for filename in glob.glob( glob_path ):
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19 fh = gzip.open( filename, 'rb' )
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20 while True:
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21 data = fh.read( CHUNK_SIZE )
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22 if data:
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23 out.write( data )
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24 else:
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25 break
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26 fh.close()
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27 if delete:
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28 os.unlink( filename )
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29 out.close()
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30
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31 def xls_to_interval( xls_file, interval_file, header = None ):
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32 out = open( interval_file, 'wb' )
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33 if header:
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34 out.write( '#%s\n' % header )
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35 wrote_header = False
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36 #From macs readme: Coordinates in XLS is 1-based which is different with BED format.
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37 #PJB: updated to keep original 'start' coordinate i.e. do not convert to BED
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38 for line in open( xls_file ):
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39 #keep all existing comment lines
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40 if line.startswith( '#' ):
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41 out.write( line )
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42 #added for macs2 since there is an extra newline
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43 ##elif line.startswith( '\n' ):
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44 ## out.write( line )
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45 elif not wrote_header:
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46 out.write( '#%s' % line )
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47 print line
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48 wrote_header = True
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49 else:
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50 fields = line.split( '\t' )
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51 if len( fields ) > 1:
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52 try:
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53 # Try to convert 'start' to int and shift
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54 ##fields[1] = str( int( fields[1] ) - 1 )
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55 # PJB don't correct, just test to see if it's an integer
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56 int( fields[1] )
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57 except ValueError:
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58 # Integer conversion failed so comment out
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59 # "bad" line instead
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60 fields[0] = "#%s" % fields[0]
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61 out.write( '\t'.join( fields ) )
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62 out.close()
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63
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64 #==========================================================================================
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65 #main
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66 #==========================================================================================
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67 def main():
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68 #take in options file and output file names
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69 options = simplejson.load( open( sys.argv[1] ) )
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70 outputs = simplejson.load( open( sys.argv[2] ) )
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71
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72 #=================================================================================
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73 #parse options and execute macs2
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74 #=================================================================================
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75 #default inputs that are in every major command
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76 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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77 cmdline = "macs2 %s -t %s" % ( options['command'], ",".join( options['input_chipseq'] ) )
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78 if options['input_control']:
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79 cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
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80
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81 #=================================================================================
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82 if (options['command'] == "callpeak"):
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83 output_summits_bed = outputs['output_summits_bed_file']
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84 output_extra_html = outputs['output_extra_file']
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85 output_extra_path = outputs['output_extra_file_path']
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86 output_peaks = outputs['output_peaks_file']
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87 output_narrowpeaks = outputs['output_narrowpeaks_file']
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88 output_broadpeaks = outputs['output_broadpeaks_file']
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89 output_gappedpeaks = outputs['output_gappedpeaks_file']
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90 output_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file']
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91 output_treat_pileup = outputs['output_treat_pileup_file']
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92 output_lambda_bedgraph = outputs['output_lambda_bedgraph_file']
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93
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94 cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s'" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'] )
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95 if (options['broad'] == 'broad'):
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96 cmdline = "%s --broad --broad-cutoff='%s'" % ( cmdline, options['broad_cutoff'] )
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97 if 'pvalue' in options:
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98 cmdline = "%s --pvalue='%s'" % ( cmdline, options['pvalue'] )
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99 elif 'qvalue' in options:
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100 cmdline = "%s --qvalue='%s'" % ( cmdline, options['qvalue'] )
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101 cmdline = "%s --mfold %s %s %s %s %s %s --keep-dup %s" % (cmdline, options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'], options['spmr'], options['call_summits'], options['keep_dup'] )
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102
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103 if 'nomodel' in options:
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104 cmdline = "%s --nomodel --extsize='%s'" % ( cmdline, options['nomodel'] )
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105 #=================================================================================
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106 if (options['command'] == "bdgcmp"):
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107 output_bdgcmp = outputs['output_bdgcmp_file']
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108
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109 cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] )
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110 #=================================================================================
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111
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112 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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113 stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report
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114 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
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115 proc.wait()
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116 #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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117 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
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118 if proc.returncode:
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119 stderr_f = open( stderr_name )
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120 while True:
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121 chunk = stderr_f.read( CHUNK_SIZE )
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122 if not chunk:
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123 stderr_f.close()
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124 break
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125 sys.stderr.write( chunk )
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126
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127 #=================================================================================
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128 #copy files created by macs2 to appripriate directory with the provided names
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129 #=================================================================================
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130
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131 #=================================================================================
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132 #move files generated by callpeak command
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133 if (options['command'] == "callpeak"):
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134 #run R to create pdf from model script
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135 if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ):
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136 cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name )
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137 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
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138 proc.wait()
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139
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140 #move bed out to proper output file
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141 created_bed_name = os.path.join( tmp_dir, "%s_summits.bed" % experiment_name )
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142 if os.path.exists( created_bed_name ):
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143 shutil.move( created_bed_name, output_summits_bed )
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144
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145 #OICR peak_xls file
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146 created_peak_xls_file = os.path.join( tmp_dir, "%s_peaks.xls" % experiment_name )
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147 if os.path.exists( created_peak_xls_file ):
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148 # 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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149 shutil.copyfile( created_peak_xls_file, output_peaks )
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150
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151 #peaks.encodepeaks (narrowpeaks) file
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152 created_narrowpeak_file = os.path.join (tmp_dir, "%s_peaks.narrowPeak" % experiment_name )
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153 if os.path.exists( created_narrowpeak_file ):
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154 shutil.move (created_narrowpeak_file, output_narrowpeaks )
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155
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156 #peaks.broadpeaks file
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157 created_broadpeak_file = os.path.join (tmp_dir, "%s_peaks.broadPeak" % experiment_name )
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158 if os.path.exists( created_broadpeak_file ):
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159 shutil.move (created_broadpeak_file, output_broadpeaks )
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160
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161 #peaks.gappedpeaks file
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162 created_gappedpeak_file = os.path.join (tmp_dir, "%s_peaks.gappedPeak" % experiment_name )
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163 if os.path.exists( created_gappedpeak_file ):
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164 shutil.move (created_gappedpeak_file, output_gappedpeaks )
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165
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166 #parse xls files to interval files as needed
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167 #if 'xls_to_interval' in options:
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168 if (options['xls_to_interval'] == "True"):
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169 create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name )
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170 if os.path.exists( create_peak_xls_file ):
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171 xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' )
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172
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173 #bedgraph bedgraph files
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174 if (options['bdg']):
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175 created_treat_pileup_file = os.path.join (tmp_dir, "%s_treat_pileup.bdg" % experiment_name )
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176 if os.path.exists( created_treat_pileup_file ):
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177 shutil.move (created_treat_pileup_file, output_treat_pileup )
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178 created_lambda_bedgraph_file = os.path.join (tmp_dir, "%s_control_lambda.bdg" % experiment_name )
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179 if os.path.exists( created_lambda_bedgraph_file ):
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180 shutil.move (created_lambda_bedgraph_file, output_lambda_bedgraph )
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181
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182 #move all remaining files to extra files path of html file output to allow user download
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183 out_html = open( output_extra_html, 'wb' )
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184 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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185 os.mkdir( output_extra_path )
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186 for filename in sorted( os.listdir( tmp_dir ) ):
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187 shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) )
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188 out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) )
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189 #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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190 out_html.write( '</ul></p>\n' )
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191 out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() )
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192 out_html.write( '</body></html>\n' )
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193 out_html.close()
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194
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195 #=================================================================================
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196 #move files generated by bdgcmp command
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197 if (options['command'] == "bdgcmp"):
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198 created_bdgcmp_file = os.path.join (tmp_dir, "bdgcmp_out.bdg" )
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199 if os.path.exists( created_bdgcmp_file ):
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200 shutil.move (created_bdgcmp_file, output_bdgcmp )
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201
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202 #=================================================================================
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203 #cleanup
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204 #=================================================================================
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205 os.unlink( stderr_name )
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206 os.rmdir( tmp_dir )
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207
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208 if __name__ == "__main__": main()
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