def test_bmtagger_empty_input(self): empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam') out_bam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([ empty_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500']) args.func_main(args) assert_equal_bam_reads(self, out_bam, empty_bam)
def test_bmtagger_empty_input(self): empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam') out_bam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args( [empty_bam, self.database_prefix_path, out_bam]) args.func_main(args) assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_bam(self): inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') outBam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([ inBam, self.database_prefix_path, outBam, '--srprismMemory', '1500']) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut)
def test_bmtagger_empty_output(self): empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam') in_bam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam') out_bam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args([ in_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500' ]) args.func_main(args) assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_bam(self): inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') outBam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args( [inBam, self.database_prefix_path, outBam]) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut)
def test_bmtagger_empty_input(self): os.environ.pop('TMPDIR', None) util.file.set_tmp_dir(None) empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam') out_bam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args([ empty_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500' ]) args.func_main(args) assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_tar_db(self): inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') outBam = util.file.mkstempfname('-out.bam') tar_db_tgz = util.file.mkstempfname('.db.tar.gz') cmd = ['tar', '-C', os.path.dirname(self.database_prefix_path), '-cvzf', tar_db_tgz, '.'] subprocess.check_call(cmd) args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([ inBam, tar_db_tgz, outBam, '--srprismMemory', '1500']) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut) os.unlink(tar_db_tgz)
def test_deplete_bmtagger_fasta_db(self): inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') ref_fasta = os.path.join(util.file.get_test_input_path(), '5kb_human_from_chr6.fasta') outBam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args( [inBam, ref_fasta, outBam, '--srprismMemory', '1500']) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut)
def test_deplete_bmtagger_bam(self): os.environ.pop('TMPDIR', None) util.file.set_tmp_dir(None) inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') outBam = util.file.mkstempfname('-out.bam') args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args([ inBam, self.database_prefix_path, outBam, '--srprismMemory', '1500' ]) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut)
def test_deplete_bmtagger_tar_db(self): inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam') outBam = util.file.mkstempfname('-out.bam') tar_db_tgz = util.file.mkstempfname('.db.tar.gz') cmd = [ 'tar', '-C', os.path.dirname(self.database_prefix_path), '-cvzf', tar_db_tgz, '.' ] subprocess.check_call(cmd) args = taxon_filter.parser_deplete_bam_bmtagger( argparse.ArgumentParser()).parse_args( [inBam, tar_db_tgz, outBam, '--srprismMemory', '1500']) args.func_main(args) expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam') assert_equal_bam_reads(self, outBam, expectedOut) os.unlink(tar_db_tgz)