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1 """
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2 Rewrite of rgFastQC.py for v. 0.11.2 of FastQC
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3
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4 """
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5 import re
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6 import os
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7 import sys
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8 import subprocess
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9 import optparse
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10 import shutil
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11 import tempfile
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12 import zipfile
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13 import gzip
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14 import glob
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15
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16 class FastQCRunner(object):
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17
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18 def __init__(self,opts=None):
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19 assert opts <> None
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20 self.opts = opts
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21
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22 def prepare_command_line(self):
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23 self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename))
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24 command_line = [opts.executable, '--outdir %s' % opts.outputdir]
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25 if opts.contaminants <> None :
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26 command_line.append('--contaminants %s' % opts.contaminants)
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27 command_line.append('--quiet %s' % self.fastqinfilename)
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28 self.command_line = ' '.join(command_line)
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29
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30 def copy_working_file_to_dataset(self):
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31 result_file = glob.glob('*html')
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32 os.system('cp %s %s' % (result_file[0], self.opts.htmloutput))
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33
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34
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35 def run_fastqc(self):
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36
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37 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
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38 sout = open(tlog, 'w')
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39
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40 self.prepare_command_line()
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41 sout.write(self.command_line)
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42 sout.write('\n')
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43 sout.write("Creating symlink\n")
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44 os.symlink(self.opts.input, self.fastqinfilename)
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45 sout.write("check_call\n")
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46 subprocess.check_call(self.command_line, shell=True)
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47 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
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48 self.copy_working_file_to_dataset()
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49 sout.write("Finished")
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50 sout.close()
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51
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52
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53 if __name__ == '__main__':
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54 op = optparse.OptionParser()
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55 op.add_option('-i', '--input', default=None)
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56 op.add_option('-j', '--inputfilename', default=None)
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57 op.add_option('-o', '--htmloutput', default=None)
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58 op.add_option('-d', '--outputdir', default="/tmp/shortread")
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59 op.add_option('-f', '--informat', default='fastq')
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60 op.add_option('-n', '--namejob', default='rgFastQC')
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61 op.add_option('-c', '--contaminants', default=None)
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62 op.add_option('-e', '--executable', default='fastqc')
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63 opts, args = op.parse_args()
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64
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65 fastqc_runner = FastQCRunner(opts)
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66 fastqc_runner.run_fastqc() |
