Example #1
0
    def process(self):
        ret_list = []
        sample_ids = []

        if type(self.input_files) != list:
            self.input_files = [self.input_files]

        for filename in self.input_files:
            for row in Fofn.get_rows(filename):
                ret_list.append(row[0])
                ret_list.append(row[1])
                sample_ids.extend(2 * [row[2]])

        self.output_files = ret_list
        self.meta["job"]["sample_id"] = sample_ids
Example #2
0
    def process(self):
        ret_list = []
        sample_ids = []

        if type(self.input_files) != list:
            self.input_files = [self.input_files]

        for filename in self.input_files:
            for row in Fofn.get_rows(filename):
                ret_list.append(row[0])
                ret_list.append(row[1])
                sample_ids.extend(2 * [row[2]])

        self.output_files = ret_list
        self.meta['job']['sample_id'] = sample_ids
Example #3
0
 def process(self):
     fofns = []
     if not hasattr(self.input_dirs, '__iter__'):
         self.input_dirs = [self.input_dirs]
     for i, idir in enumerate(self.input_dirs):
         sample_sheet = ''
         if self.input_files:
             sample_sheet = self.input_files[i]
         else:
             sample_sheet = os.path.join(idir, self.ss_name)
         ifofn = 'fofn_%03d.csv' % i
         fofns.append(
             Fofn.create(sample_sheet, idir, self.output_dir, ifofn))
     mfofn = os.path.join(self.output_dir, self.output_files)
     with open(mfofn, 'w') as ofh:
         for fofn in fofns:
             with open(fofn) as ifh:
                 ofh.write(''.join(ifh.readlines()))
             os.remove(fofn)
     self.output_files = [mfofn]
Example #4
0
 def process(self):
     fofns = []
     if not hasattr(self.input_dirs, '__iter__'):
         self.input_dirs = [self.input_dirs]
     for i, idir in enumerate(self.input_dirs):
         sample_sheet = ''
         if self.input_files:
             sample_sheet = self.input_files[i]
         else:
             sample_sheet = os.path.join(idir, self.ss_name)           
         ifofn = 'fofn_%03d.csv' % i
         fofns.append(Fofn.create(
                             sample_sheet,
                             idir,
                             self.output_dir,
                             ifofn)
                     )
     mfofn = os.path.join(self.output_dir, self.output_files)
     with open(mfofn, 'w') as ofh:
         for fofn in fofns:
             with open(fofn) as ifh:
                 ofh.write( ''.join(ifh.readlines()) )
             os.remove(fofn)
     self.output_files = [mfofn]