def test_partition_bmtagger(self): outMatch = [ os.path.join(self.tempDir, 'outMatch.{}.fastq'.format(n)) for n in '12' ] outNoMatch = [ os.path.join(self.tempDir, 'outNoMatch.{}.fastq'.format(n)) for n in '12' ] myInputDir = util.file.get_test_input_path(self) args = taxon_filter.parser_partition_bmtagger( argparse.ArgumentParser()).parse_args([ os.path.join(myInputDir, 'in1.fastq'), os.path.join(myInputDir, 'in2.fastq'), os.path.join(self.tempDir, 'humanChr1Subset'), os.path.join(self.tempDir, 'humanChr9Subset'), '--outMatch', outMatch[0], outMatch[1], '--outNoMatch', outNoMatch[0], outNoMatch[1] ]) args.func_main(args) # Compare to expected for case in ['Match.1', 'Match.2', 'NoMatch.1', 'NoMatch.2']: assert_equal_contents( self, os.path.join(self.tempDir, 'out' + case + '.fastq'), os.path.join(myInputDir, 'expected.' + case + '.fastq'))
def test_deplete_bmtagger(self): myInputDir = util.file.get_test_input_path(self) args = taxon_filter.parser_partition_bmtagger(argparse.ArgumentParser()).parse_args( [os.path.join(myInputDir, 'in1.fastq'), os.path.join(myInputDir, 'in2.fastq'), os.path.join( self.tempDir, 'humanChr1Subset'), os.path.join(self.tempDir, 'humanChr9Subset'), '--outNoMatch', os.path.join(self.tempDir, 'deplete.1.fastq'), os.path.join(self.tempDir, 'deplete.2.fastq')]) args.func_main(args) # Compare to expected for case in ['1', '2']: assert_equal_contents(self, os.path.join(self.tempDir, 'deplete.' + case + '.fastq'), os.path.join(myInputDir, 'expected.NoMatch.' + case + '.fastq'))
def test_partition_bmtagger(self): outMatch = [os.path.join(self.tempDir, 'outMatch.{}.fastq'.format(n)) for n in '12'] outNoMatch = [os.path.join(self.tempDir, 'outNoMatch.{}.fastq'.format(n)) for n in '12'] myInputDir = util.file.get_test_input_path(self) args = taxon_filter.parser_partition_bmtagger(argparse.ArgumentParser()).parse_args( [os.path.join(myInputDir, 'in1.fastq'), os.path.join(myInputDir, 'in2.fastq'), os.path.join( self.tempDir, 'humanChr1Subset'), os.path.join(self.tempDir, 'humanChr9Subset'), '--outMatch', outMatch[0], outMatch[1], '--outNoMatch', outNoMatch[0], outNoMatch[1]]) args.func_main(args) # Compare to expected for case in ['Match.1', 'Match.2', 'NoMatch.1', 'NoMatch.2']: assert_equal_contents(self, os.path.join(self.tempDir, 'out' + case + '.fastq'), os.path.join(myInputDir, 'expected.' + case + '.fastq'))