Mercurial > repos > devteam > fastqc

comparison rgFastQC.py @ 12:919cf12bb71c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
author iuc
date Mon, 23 Oct 2017 13:23:42 -0400
parents 0a7c65540937
children
comparison
equal deleted inserted replaced
11:f5a25a56ab9d 12:919cf12bb71c
56 if linf.endswith('.gz') or linf.endswith('.gzip') or ftype[-1] == "gzip" or informat.endswith('.gz'): 56 if linf.endswith('.gz') or linf.endswith('.gzip') or ftype[-1] == "gzip" or informat.endswith('.gz'):
57 f = gzip.open(self.opts.input) 57 f = gzip.open(self.opts.input)
58 try: 58 try:
59 f.readline() 59 f.readline()
60 ftype = ['gzip'] 60 ftype = ['gzip']
61 except: 61 except Exception:
62 trimext = True 62 trimext = True
63 f.close() 63 f.close()
64 elif linf.endswith('bz2') or informat.endswith('.bz2'): 64 elif linf.endswith('bz2') or informat.endswith('.bz2'):
65 f = bz2.BZ2File(self.opts.input, 'r') 65 f = bz2.BZ2File(self.opts.input, 'r')
66 try: 66 try:
67 ftype = ['bzip2'] 67 ftype = ['bzip2']
68 f.readline() 68 f.readline()
69 except: 69 except Exception:
70 trimext = True 70 trimext = True
71 f.close() 71 f.close()
72 elif linf.endswith('.zip'): 72 elif linf.endswith('.zip'):
73 if not zipfile.is_zipfile(self.opts.input): 73 if not zipfile.is_zipfile(self.opts.input):
74 trimext = True 74 trimext = True
75 if trimext: 75 if trimext:
76 f = open(self.opts.input) 76 f = open(self.opts.input)
77 try: 77 try:
78 f.readline() 78 f.readline()
79 except: 79 except Exception:
80 raise Exception("Input file corruption, could not identify the filetype") 80 raise Exception("Input file corruption, could not identify the filetype")
81 infname = os.path.splitext(infname)[0] 81 infname = os.path.splitext(infname)[0]
82 82
83 # Replace unwanted or problematic charaters in the input file name 83 # Replace unwanted or problematic charaters in the input file name
84 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname)) 84 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))