def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) otu_files = map(open, opts.otu_map_fps) failures_fp = opts.failures_fp output_fp = opts.output_fp if failures_fp: failures_f = open(failures_fp, 'U') else: failures_f = None try: result = map_otu_map_files(otu_files, failures_file=failures_f) except KeyError as e: print( 'Some keys do not map (' + str(e) + ') -- is the order of' ' your OTU maps equivalent to the order in which the OTU pickers' ' were run? If expanding a failures file, did you remember to leave' ' out the otu map from the run which generated the failures file?') exit(1) if failures_fp is not None: of = open(output_fp, 'w') of.write('\n'.join(result)) of.close() else: write_otu_map(result.items(), output_fp)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) otu_files = map(open, opts.otu_map_fps) failures_fp = opts.failures_fp output_fp = opts.output_fp if failures_fp: failures_f = open(failures_fp, 'U') else: failures_f = None try: result = map_otu_map_files(otu_files, failures_file=failures_f) except KeyError as e: print ('Some keys do not map (' + str(e) + ') -- is the order of' ' your OTU maps equivalent to the order in which the OTU pickers' ' were run? If expanding a failures file, did you remember to leave' ' out the otu map from the run which generated the failures file?') exit(1) if failures_fp is not None: of = open(output_fp, 'w') of.write('\n'.join(result)) of.close() else: write_otu_map(result.items(), output_fp)
def test_write_otu_map_prefix(self): """write_otu_map functions as expected w otu prefix """ write_otu_map(self.otu_map1, self.tmp_fp1, "my.otu.") actual = fields_to_dict(open(self.tmp_fp1)) self.files_to_remove.append(self.tmp_fp1) exp = {"my.otu.0": ["seq1", "seq2", "seq5"], "my.otu.1": ["seq3", "seq4"], "my.otu.2": ["seq6", "seq7", "seq8"]} self.assertEqual(actual, exp)
def test_write_otu_map_prefix(self): """write_otu_map functions as expected w otu prefix """ write_otu_map(self.otu_map1,self.tmp_fp1,'my.otu.') actual = fields_to_dict(open(self.tmp_fp1)) self.files_to_remove.append(self.tmp_fp1) exp = {'my.otu.0':['seq1','seq2','seq5'], 'my.otu.1':['seq3','seq4'], 'my.otu.2':['seq6','seq7','seq8']} self.assertEqual(actual,exp)
def test_write_otu_map_prefix(self): """write_otu_map functions as expected w otu prefix """ write_otu_map(self.otu_map1, self.tmp_fp1, 'my.otu.') actual = fields_to_dict(open(self.tmp_fp1)) self.files_to_remove.append(self.tmp_fp1) exp = {'my.otu.0': ['seq1', 'seq2', 'seq5'], 'my.otu.1': ['seq3', 'seq4'], 'my.otu.2': ['seq6', 'seq7', 'seq8']} self.assertEqual(actual, exp)
def test_write_otu_map(self): """write_otu_map functions as expected """ write_otu_map(self.otu_map1, self.tmp_fp1) actual = fields_to_dict(open(self.tmp_fp1)) self.files_to_remove.append(self.tmp_fp1) self.assertEqual(actual, dict(self.otu_map1))
def test_write_otu_map(self): """write_otu_map functions as expected """ write_otu_map(self.otu_map1,self.tmp_fp1) actual = fields_to_dict(open(self.tmp_fp1)) self.files_to_remove.append(self.tmp_fp1) self.assertEqual(actual,dict(self.otu_map1))
option_parser, opts, args =\ parse_command_line_parameters(**script_info) otu_files = map(open,opts.otu_map_fps) failures_fp = opts.failures_fp output_fp = opts.output_fp if failures_fp: failures_f = open(failures_fp,'U') else: failures_f = None try: result = map_otu_map_files(otu_files,failures_file=failures_f) except KeyError,e: print ('Some keys do not map ('+ str(e) +') -- is the order of' ' your OTU maps equivalent to the order in which the OTU pickers' ' were run? If expanding a failures file, did you remember to leave' ' out the otu map from the run which generated the failures file?') exit(1) if failures_fp != None: of = open(output_fp,'w') of.write('\n'.join(result)) of.close() else: write_otu_map(result.items(),output_fp) if __name__ == "__main__": main()