comparison rgFastQC.py @ 4:8c650f7f76e9 draft

Uploaded

3:0b201de108b9

	       raise Exception("Input file corruption, could not identify the filetype")
           infname = os.path.splitext(infname)[0]
        
        # Replace unwanted or problematic charaters in the input file name
        self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
        
        # Build the Commandline from the given parameters
        command_line = [opts.executable, '--outdir %s' % opts.outputdir]
        if opts.contaminants != None:
            command_line.append('--contaminants %s' % opts.contaminants)
        if opts.limits != None:
	    command_line.append('--limits %s' % opts.limits)
        command_line.append('--quiet')
        command_line.append('--extract') # to access the output text file
        command_line.append(self.fastqinfilename)
        self.command_line = ' '.join(command_line)

    def copy_output_file_to_dataset(self):
        '''
        Retrieves the output html and text files from the output directory and copies them to the Galaxy output files

4:8c650f7f76e9

	       raise Exception("Input file corruption, could not identify the filetype")
           infname = os.path.splitext(infname)[0]
        
        # Replace unwanted or problematic charaters in the input file name
        self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
        # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
        if 'fastq' in opts.informat:
            # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's 
            # accepted formats..
            opts.informat = 'fastq'
        elif not self.fastqinfilename.endswith(opts.informat):
            self.fastqinfilename += '.%s' % opts.informat

        # Build the Commandline from the given parameters
        command_line = [opts.executable, '--outdir %s' % opts.outputdir]
        if opts.contaminants != None:
            command_line.append('--contaminants %s' % opts.contaminants)
        if opts.limits != None:
	    command_line.append('--limits %s' % opts.limits)
        command_line.append('--quiet')
        command_line.append('--extract') # to access the output text file
        command_line.append(self.fastqinfilename)
        command_line.append('-f %s' % opts.informat)
        self.command_line = ' '.join(command_line)

    def copy_output_file_to_dataset(self):
        '''
        Retrieves the output html and text files from the output directory and copies them to the Galaxy output files