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annotate FastQC/rgFastQC.py @ 0:42251cbdeeac draft

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Initial commit of test for FastQC with installation of the java stuff
author fubar
date Mon, 03 Jun 2013 20:30:24 -0400
parents
children 91cb2603b56c
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1 """
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2 # May 2013 ross added check for bogus gz extension - fastqc gets confused
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3 # added sanitizer for user supplied name
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4 # removed shell and make cl a sequence for Popen call
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5 # ross lazarus August 10 2012 in response to anon insecurity report
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6 wrapper for fastqc
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7
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8 called as
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9 <command interpreter="python">
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10 rgFastqc.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix"
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11 </command>
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12
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13
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14
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15 Current release seems overly intolerant of sam/bam header strangeness
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16 Author notified...
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17
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18
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19 """
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20 import re
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21 import os
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22 import sys
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23 import subprocess
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24 import optparse
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25 import shutil
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26 import tempfile
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27 from rgutils import getFileString
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28 import zipfile
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29 import gzip
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30
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31 class FastQC():
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32 """wrapper
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33 """
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34
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35
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36 def __init__(self,opts=None):
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37 assert opts <> None
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38 self.opts = opts
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39
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40
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41 def run_fastqc(self):
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42 """
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43 In batch mode fastqc behaves not very nicely - will write to a new folder in
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44 the same place as the infile called [infilebasename]_fastqc
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45 rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc
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46 duplication_levels.png fastqc_icon.png per_base_n_content.png per_sequence_gc_content.png summary.txt
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47 error.png fastqc_report.html per_base_quality.png per_sequence_quality.png tick.png
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48 fastqc_data.txt per_base_gc_content.png per_base_sequence_content.png sequence_length_distribution.png warning.png
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49
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50 """
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51 serr = ''
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52 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
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53 sout = open(tlog, 'w')
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54 fastq = os.path.basename(self.opts.input)
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55 cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir]
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56 if self.opts.informat in ['sam','bam']:
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57 cl.append('--f=%s' % self.opts.informat)
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58 if self.opts.contaminants <> None :
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59 cl.append('--contaminants=%s' % self.opts.contaminants)
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60 # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
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61 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name
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62 # note this exposes a bug in the EBI_SRA download tool which leaves bogus .gz extensions on uncompressed files
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63 # which fastqc helpfully tries to uncompress again - hilarity ensues.
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64 # patched may 29 2013 until this is fixed properly
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65 infname = self.opts.inputfilename
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66 linf = infname.lower()
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67 trimext = False
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68 if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
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69 f = gzip.open(self.opts.input)
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70 try:
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71 testrow = f.readline()
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72 except:
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73 trimext = True
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74 f.close()
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75 elif linf.endswith('bz2'):
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76 f = bz2.open(self.opts.input,'rb')
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77 try:
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78 f.readline()
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79 except:
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80 trimext = True
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81 f.close()
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82 elif linf.endswith('.zip'):
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83 if not zipfile.is_zipfile(self.opts.input):
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84 trimext = True
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85 if trimext:
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86 infname = os.path.splitext(infname)[0]
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87 fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
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88 link_name = os.path.join(self.opts.outputdir, fastqinfilename)
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89 os.symlink(self.opts.input, link_name)
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90 cl.append(link_name)
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91 sout.write('# FastQC cl = %s\n' % ' '.join(cl))
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92 sout.flush()
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93 p = subprocess.Popen(cl, shell=False, stderr=sout, stdout=sout, cwd=self.opts.outputdir)
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94 retval = p.wait()
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95 sout.close()
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96 runlog = open(tlog,'r').readlines()
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97 os.unlink(link_name)
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98 flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh
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99 odpath = None
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100 for f in flist:
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101 d = os.path.join(self.opts.outputdir,f)
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102 if os.path.isdir(d):
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103 if d.endswith('_fastqc'):
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104 odpath = d
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105 hpath = None
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106 if odpath <> None:
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107 try:
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108 hpath = os.path.join(odpath,'fastqc_report.html')
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109 rep = open(hpath,'r').readlines() # for our new html file but we need to insert our stuff after the <body> tag
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110 except:
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111 pass
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112 if hpath == None:
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113 serr = '\n'.join(runlog)
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114 res = ['## odpath=%s: No output found in %s. Output for the run was:<pre>\n' % (odpath,hpath),]
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115 res += runlog
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116 res += ['</pre>\n',
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117 'Please read the above for clues<br/>\n',
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118 'If you selected a sam/bam format file, it might not have headers or they may not start with @HD?<br/>\n',
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119 'It is also possible that the log shows that fastqc is not installed?<br/>\n',
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120 'If that is the case, please tell the relevant Galaxy administrator that it can be snarfed from<br/>\n',
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121 'http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/<br/>\n',]
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122 return res,1,serr
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123 self.fix_fastqcimages(odpath)
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124 flist = os.listdir(self.opts.outputdir) # these have now been fixed
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125 excludefiles = ['tick.png','warning.png','fastqc_icon.png','error.png']
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126 flist = [x for x in flist if not x in excludefiles]
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127 for i in range(len(rep)): # need to fix links to Icons and Image subdirectories in lastest fastqc code - ugh
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128 rep[i] = rep[i].replace('Icons/','')
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129 rep[i] = rep[i].replace('Images/','')
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130 html = self.fix_fastqc(rep,flist,runlog)
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131 return html,retval,serr
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132
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133
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134
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135 def fix_fastqc(self,rep=[],flist=[],runlog=[]):
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136 """ add some of our stuff to the html
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137 """
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138 bodyindex = len(rep) -1 # hope they don't change this
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139 footrow = bodyindex - 1
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140 footer = rep[footrow]
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141 rep = rep[:footrow] + rep[footrow+1:]
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142 res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n']
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143 flist.sort()
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144 for i,f in enumerate(flist):
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145 if not(os.path.isdir(f)):
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146 fn = os.path.split(f)[-1]
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147 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir)))
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148 res.append('</table>\n')
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149 res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
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150 res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>')
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151 res.append(footer)
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152 fixed = rep[:bodyindex] + res + rep[bodyindex:]
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153 return fixed # with our additions
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154
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155
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156 def fix_fastqcimages(self,odpath):
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157 """ Galaxy wants everything in the same files_dir
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158 """
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159 icpath = os.path.join(odpath,'Icons')
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160 impath = os.path.join(odpath,'Images')
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161 for adir in [icpath,impath,odpath]:
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162 if os.path.exists(adir):
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163 flist = os.listdir(adir) # get all files created
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164 for f in flist:
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165 if not os.path.isdir(os.path.join(adir,f)):
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166 sauce = os.path.join(adir,f)
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167 dest = os.path.join(self.opts.outputdir,f)
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168 shutil.move(sauce,dest)
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169 os.rmdir(adir)
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170
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171
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172
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173 if __name__ == '__main__':
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174 op = optparse.OptionParser()
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175 op.add_option('-i', '--input', default=None)
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176 op.add_option('-j', '--inputfilename', default=None)
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177 op.add_option('-o', '--htmloutput', default=None)
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178 op.add_option('-d', '--outputdir', default="/tmp/shortread")
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179 op.add_option('-f', '--informat', default='fastq')
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180 op.add_option('-n', '--namejob', default='rgFastQC')
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181 op.add_option('-c', '--contaminants', default=None)
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182 op.add_option('-e', '--executable', default='fastqc')
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183 opts, args = op.parse_args()
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184 assert opts.input <> None
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185 assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
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186 if not os.path.exists(opts.outputdir):
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187 os.makedirs(opts.outputdir)
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188 f = FastQC(opts)
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189 html,retval,serr = f.run_fastqc()
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190 f = open(opts.htmloutput, 'w')
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191 f.write(''.join(html))
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192 f.close()
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193 if retval <> 0:
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194 print >> sys.stderr, serr # indicate failure
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195
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196
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197