Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

comparison scripts/rgFastQC.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
comparison
equal deleted inserted replaced
2:6837f733b4aa 3:0cbed1c0a762
68 f.close() 68 f.close()
69 elif linf.endswith('.zip'): 69 elif linf.endswith('.zip'):
70 if not zipfile.is_zipfile(self.opts.input): 70 if not zipfile.is_zipfile(self.opts.input):
71 trimext = True 71 trimext = True
72 if trimext: 72 if trimext:
73 f = open(self.opts.input) 73 f = open(self.opts.input)
74 try: 74 try:
75 f.readline() 75 f.readline()
76 except: 76 except:
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(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise 82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
83 if 'fastq' in opts.informat: 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 84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
85 # accepted formats.. 85 # accepted formats..
86 opts.informat = 'fastq' 86 opts.informat = 'fastq'
90 # Build the Commandline from the given parameters 90 # Build the Commandline from the given parameters
91 command_line = [opts.executable, '--outdir %s' % opts.outputdir] 91 command_line = [opts.executable, '--outdir %s' % opts.outputdir]
92 if opts.contaminants != None: 92 if opts.contaminants != None:
93 command_line.append('--contaminants %s' % opts.contaminants) 93 command_line.append('--contaminants %s' % opts.contaminants)
94 if opts.limits != None: 94 if opts.limits != None:
95 command_line.append('--limits %s' % opts.limits) 95 command_line.append('--limits %s' % opts.limits)
96 command_line.append('--quiet') 96 command_line.append('--quiet')
97 command_line.append('--extract') # to access the output text file 97 command_line.append('--extract') # to access the output text file
98 command_line.append(self.fastqinfilename) 98 command_line.append(self.fastqinfilename)
99 command_line.append('-f %s' % opts.informat) 99 command_line.append('-f %s' % opts.informat)
100 self.command_line = ' '.join(command_line) 100 self.command_line = ' '.join(command_line)