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comparison rgFastQC.py @ 4:8c650f7f76e9 draft

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Uploaded
author devteam
date Mon, 09 Feb 2015 09:56:10 -0500
parents 0b201de108b9
children 3fdc1a74d866
comparison
equal deleted inserted replaced
3:0b201de108b9 4:8c650f7f76e9
77 raise Exception("Input file corruption, could not identify the filetype") 77 raise Exception("Input file corruption, could not identify the filetype")
78 infname = os.path.splitext(infname)[0] 78 infname = os.path.splitext(infname)[0]
79 79
80 # Replace unwanted or problematic charaters in the input file name 80 # Replace unwanted or problematic charaters in the input file name
81 self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname)) 81 self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
82 82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
83 if 'fastq' in opts.informat:
84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
85 # accepted formats..
86 opts.informat = 'fastq'
87 elif not self.fastqinfilename.endswith(opts.informat):
88 self.fastqinfilename += '.%s' % opts.informat
89
83 # Build the Commandline from the given parameters 90 # Build the Commandline from the given parameters
84 command_line = [opts.executable, '--outdir %s' % opts.outputdir] 91 command_line = [opts.executable, '--outdir %s' % opts.outputdir]
85 if opts.contaminants != None: 92 if opts.contaminants != None:
86 command_line.append('--contaminants %s' % opts.contaminants) 93 command_line.append('--contaminants %s' % opts.contaminants)
87 if opts.limits != None: 94 if opts.limits != None:
88 command_line.append('--limits %s' % opts.limits) 95 command_line.append('--limits %s' % opts.limits)
89 command_line.append('--quiet') 96 command_line.append('--quiet')
90 command_line.append('--extract') # to access the output text file 97 command_line.append('--extract') # to access the output text file
91 command_line.append(self.fastqinfilename) 98 command_line.append(self.fastqinfilename)
99 command_line.append('-f %s' % opts.informat)
92 self.command_line = ' '.join(command_line) 100 self.command_line = ' '.join(command_line)
93 101
94 def copy_output_file_to_dataset(self): 102 def copy_output_file_to_dataset(self):
95 ''' 103 '''
96 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files 104 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files