Python multi_db_deplete_bam Exemples

Exemple #1

 def test_blastn_empty_input(self):
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     out_bam = util.file.mkstempfname('-out.bam')
     taxon_filter.multi_db_deplete_bam(empty_bam, [self.blastdb_path],
                                       taxon_filter.deplete_blastn_bam,
                                       out_bam)
     self.assertEqual(0, tools.samtools.SamtoolsTool().count(out_bam))

Exemple #2

Fichier : test_taxon_filter.py Projet : flyfl1992/viral-ngs

 def test_blastn_empty_input(self):
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     out_bam = util.file.mkstempfname('-out.bam')
     taxon_filter.multi_db_deplete_bam(empty_bam, [self.blastdb_path],
                                       taxon_filter.deplete_blastn_bam,
                                       out_bam)
     assert_equal_bam_reads(self, out_bam, empty_bam)

Exemple #3

Fichier : test_taxon_filter.py Projet : yesimon/viral-ngs

 def test_blastn_empty_output(self):
     in_bam = os.path.join(util.file.get_test_input_path(self), 'test-reads-human.bam')
     taxon_filter.multi_db_deplete_bam(
         in_bam,
         [self.blastdb_path],
         taxon_filter.deplete_blastn_bam,
         util.file.mkstempfname()
     )

Exemple #4

Fichier : test_taxon_filter.py Projet : yesimon/viral-ngs

 def test_blastn_empty_input(self):
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     taxon_filter.multi_db_deplete_bam(
         empty_bam,
         [self.blastdb_path],
         taxon_filter.deplete_blastn_bam,
         util.file.mkstempfname()
     )

Exemple #5

Fichier : test_taxon_filter.py Projet : yesimon/viral-ngs

 def test_bmtagger_empty_output(self):
     in_bam = os.path.join(util.file.get_test_input_path(self), 'test-reads-human.bam')
     taxon_filter.multi_db_deplete_bam(
         in_bam,
         [self.database_prefix_path],
         taxon_filter.deplete_bmtagger_bam,
         util.file.mkstempfname()
     )

Exemple #6

Fichier : test_taxon_filter.py Projet : yesimon/viral-ngs

 def test_bmtagger_empty_input(self):
     empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
     taxon_filter.multi_db_deplete_bam(
         empty_bam,
         [self.database_prefix_path],
         taxon_filter.deplete_bmtagger_bam,
         util.file.mkstempfname()
     )

Exemple #7

Fichier : test_taxon_filter.py Projet : broadinstitute/viral-ngs

 def test_blastn_empty_output(self):
     in_bam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')
     out_bam = util.file.mkstempfname('-out.bam')
     taxon_filter.multi_db_deplete_bam(
         in_bam,
         [self.blastdb_path],
         taxon_filter.deplete_blastn_bam,
         out_bam
     )
     self.assertEqual(0, tools.samtools.SamtoolsTool().count(out_bam))