Mercurial > repos > pjbriggs > macs21

annotate macs21_wrapper.py @ 1:d0986d2be693 draft

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Substantial reimplementation of internals, also renamed id and version.
author pjbriggs
date Thu, 29 Jan 2015 11:11:21 -0500
parents fdad0c8c0957
children 15889783e759
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1 #!/bin/env python
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2 #
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3 # Galaxy wrapper to run MACS 2.1
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4 #
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5 # Completely rewritten from the original macs2 wrapped by Ziru Zhou
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6 # taken from http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
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7
1
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8 import sys
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9 import os
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10 import subprocess
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11 import tempfile
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12 import shutil
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13
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14 def move_file(working_dir,name,destination):
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15 """Move a file 'name' from 'working_dir' to 'destination'
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16
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17 """
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18 if destination is None:
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19 # Nothing to do
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20 return
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21 source = os.path.join(working_dir,name)
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22 if os.path.exists(source):
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23 shutil.move(source,destination)
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24
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25 def convert_xls_to_interval(xls_file,interval_file,header=None):
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26 """Convert MACS XLS file to interval
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27
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28 From the MACS readme: "Coordinates in XLS is 1-based which is different with
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29 BED format."
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30
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31 However this function no longer performs any coordinate conversions, it
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32 simply ensures that any blank or non-data lines are commented out
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33
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34 """
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35 fp = open(interval_file,'wb')
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36 if header:
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37 fp.write('#%s\n' % header)
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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 fp.write(line)
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42 else:
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43 # Split line into fields and test to see if
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44 # the 'start' field is actually an integer
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45 fields = line.split('\t')
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46 if len(fields) > 1:
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47 try:
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48 int(fields[1])
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49 except ValueError:
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50 # Integer conversion failed so comment out
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51 # "bad" line instead
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52 fields[0] = "#%s" % fields[0]
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53 fp.write( '\t'.join( fields ) )
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54 fp.close()
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55
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56 if __name__ == "__main__":
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57
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58 # Echo the command line
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59 print ' '.join(sys.argv)
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60
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61 # Initialise output files - values are set by reading from
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62 # the command line supplied by the Galaxy wrapper
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63 output_extra_html = None
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64 output_extra_path = None
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65 output_broadpeaks = None
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66 output_gappedpeaks = None
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67 output_narrowpeaks = None
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68 output_treat_pileup = None
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69 output_lambda_bedgraph = None
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70 output_xls_to_interval_peaks_file = None
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71 output_peaks = None
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72 output_bdgcmp = None
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73
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74 # Build the MACS 2.1 command line
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75 # Initial arguments are always the same: command & input ChIP-seq file name
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76 cmdline = ["macs2 %s -t %s" % (sys.argv[1],sys.argv[2])]
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77
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78 # Process remaining args
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79 for arg in sys.argv[3:]:
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80 if arg.startswith('--format='):
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81 # Convert format to uppercase
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82 format_ = arg.split('=')[1].upper()
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83 cmdline.append("--format=%s" % format_)
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84 elif arg.startswith('--name='):
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85 # Replace whitespace in name with underscores
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86 experiment_name = '_'.join(arg.split('=')[1].split())
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87 cmdline.append("--name=%s" % experiment_name)
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88 elif arg.startswith('--output-'):
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89 # Handle destinations for output files
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90 arg0,filen = arg.split('=')
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91 if arg0 == '--output-summits':
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92 output_summits = filen
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93 elif arg0 == '--output-extra-files':
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94 output_extra_html = filen
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95 elif arg0 == '--output-extra-files-path':
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96 output_extra_path = filen
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97 elif arg0 == '--output-broadpeaks':
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98 output_broadpeaks = filen
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99 elif arg0 == '--output-gappedpeaks':
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100 output_gappedpeaks = filen
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101 elif arg0 == '--output-narrowpeaks':
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102 output_narrowpeaks = filen
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103 elif arg0 == '--output-pileup':
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104 output_treat_pileup = filen
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105 elif arg0 == '--output-lambda-bedgraph':
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106 output_lambda_bedgraph = filen
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107 elif arg0 == '--output-xls-to-interval':
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108 output_xls_to_interval_peaks_file = filen
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109 elif arg0 == '--output-peaks':
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110 output_peaks = filen
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111 else:
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112 # Pass remaining args directly to MACS
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113 # command line
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114 cmdline.append(arg)
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115
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116 cmdline = ' '.join(cmdline)
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117 print "Generated command line:\n%s" % cmdline
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118
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119 # Execute MACS2
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120 #
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121 # Make a working directory
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122 working_dir = tempfile.mkdtemp()
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123 #
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124 # Collect stderr in a file for reporting later
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125 stderr_filen = tempfile.NamedTemporaryFile().name
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126 #
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127 # Run MACS2
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128 proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir,
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129 stderr=open(stderr_filen,'wb'))
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130 proc.wait()
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131
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132 # Run R script to create PDF from model script
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133 if os.path.exists(os.path.join(working_dir,"%s_model.r" % experiment_name)):
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134 cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % \
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135 (experiment_name, experiment_name)
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136 proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir)
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137 proc.wait()
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138
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139 # Convert XLS to interval, if requested
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140 if output_xls_to_interval_peaks_file is not None:
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141 peaks_xls_file = os.path.join(working_dir,'%s_peaks.xls' % experiment_name )
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142 if os.path.exists(peaks_xls_file):
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143 convert_xls_to_interval(peaks_xls_file,output_xls_to_interval_peaks_file,
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144 header='peaks file')
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145
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146 # Move MACS2 output files from working dir to their final destinations
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147 move_file(working_dir,"%s_summits.bed" % experiment_name,output_summits)
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148 move_file(working_dir,"%s_peaks.xls" % experiment_name,output_peaks)
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149 move_file(working_dir,"%s_peaks.narrowPeak" % experiment_name,output_narrowpeaks)
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150 move_file(working_dir,"%s_peaks.broadPeak" % experiment_name,output_broadpeaks)
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151 move_file(working_dir,"%s_peaks.gappedPeak" % experiment_name,output_gappedpeaks)
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152 move_file(working_dir,"%s_treat_pileup.bdg" % experiment_name,output_treat_pileup)
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153 move_file(working_dir,"%s_control_lambda.bdg" % experiment_name,output_lambda_bedgraph)
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154 move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp)
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155
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156 # Move remaining file to the 'extra files' path and link from the HTML
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157 # file to allow user to access them from within Galaxy
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158 html_file = open(output_extra_html,'wb')
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159 html_file.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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160 # Make the 'extra files' directory
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161 os.mkdir(output_extra_path)
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162 # Move the files
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163 for filen in sorted(os.listdir(working_dir)):
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164 shutil.move(os.path.join(working_dir,filen),
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165 os.path.join(output_extra_path,filen))
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166 html_file.write( '<li><a href="%s">%s</a></li>\n' % (filen,filen))
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167 # All files moved, close out HTML
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168 html_file.write( '</ul></p>\n' )
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169 # Append any stderr output
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170 html_file.write('<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' %
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171 open(stderr_filen,'rb').read())
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172 html_file.write('</body></html>\n')
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173 html_file.close()
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174
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175 # Clean up the working directory and files
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176 os.unlink(stderr_filen)
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177 os.rmdir(working_dir)