Mercurial > repos > devteam > fastqc

comparison rgFastQC.py @ 11:db2dc6bc8f05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 168f7aeb0f9f38de6dec873f3cbf0c30014fdd72
author iuc
date Thu, 20 Apr 2017 11:06:17 -0400
parents a00a6402d09a
children f2e8552cf1d0
comparison
equal deleted inserted replaced
10:a00a6402d09a 11:db2dc6bc8f05
46 46
47 # Check whether a given file compression format is valid 47 # Check whether a given file compression format is valid
48 # This prevents uncompression of already uncompressed files 48 # This prevents uncompression of already uncompressed files
49 infname = self.opts.inputfilename 49 infname = self.opts.inputfilename
50 linf = infname.lower() 50 linf = infname.lower()
51 informat = self.opts.informat
51 trimext = False 52 trimext = False
52 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf 53 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
53 # patched may 29 2013 until this is fixed properly 54 # patched may 29 2013 until this is fixed properly
54 type = mimetypes.guess_type(self.opts.input) 55 ftype = mimetypes.guess_type(self.opts.input)
55 if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip": 56 if linf.endswith('.gz') or linf.endswith('.gzip') or ftype[-1] == "gzip" or informat.endswith('.gz'):
56 f = gzip.open(self.opts.input) 57 f = gzip.open(self.opts.input)
57 try: 58 try:
58 f.readline() 59 f.readline()
60 ftype = ['gzip']
59 except: 61 except:
60 trimext = True 62 trimext = True
61 f.close() 63 f.close()
62 elif linf.endswith('bz2'): 64 elif linf.endswith('bz2') or informat.endswith('.bz2'):
63 f = bz2.BZ2File(self.opts.input, 'r') 65 f = bz2.BZ2File(self.opts.input, 'r')
64 try: 66 try:
67 ftype = ['bzip2']
65 f.readline() 68 f.readline()
66 except: 69 except:
67 trimext = True 70 trimext = True
68 f.close() 71 f.close()
69 elif linf.endswith('.zip'): 72 elif linf.endswith('.zip'):
93 command_line.append('--contaminants %s' % self.opts.contaminants) 96 command_line.append('--contaminants %s' % self.opts.contaminants)
94 if self.opts.limits is not None: 97 if self.opts.limits is not None:
95 command_line.append('--limits %s' % self.opts.limits) 98 command_line.append('--limits %s' % self.opts.limits)
96 command_line.append('--quiet') 99 command_line.append('--quiet')
97 command_line.append('--extract') # to access the output text file 100 command_line.append('--extract') # to access the output text file
98 if type[-1] != "gzip": 101 if ftype[-1] == 'gzip':
102 self.fastqinfilename += '.gz'
103 elif ftype[-1] == 'bzip2':
104 self.fastqinfilename += '.bz2'
105 else:
99 command_line.append('-f %s' % self.opts.informat) 106 command_line.append('-f %s' % self.opts.informat)
100 else:
101 self.fastqinfilename += ".gz"
102 command_line.append(self.fastqinfilename) 107 command_line.append(self.fastqinfilename)
103 self.command_line = ' '.join(command_line) 108 self.command_line = ' '.join(command_line)
104 109
105 def copy_output_file_to_dataset(self): 110 def copy_output_file_to_dataset(self):
106 ''' 111 '''