def test_index(self): """Test for creating index files for the reference genome fasta file""" cmdline = BwaIndexCommandline() cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm","bwtsw") stdout,stderr = cmdline() output = stdout.startswith("[bwt_gen]") self.assertTrue(stdout.startswith("[bwt_gen]"), "FASTA indexing failed:\n%s\nStdout:%s" \ % (cmdline, stdout))
def create_fasta_index(self): """Creates index for fasta file. BWA requires an indexed fasta for each alignment operation. This should be called to create an index before any alignment operation. """ cmdline = BwaIndexCommandline(bwa_exe) cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline()
def test_index(self): """Test for creating index files for the reference genome fasta file""" cmdline = BwaIndexCommandline(bwa_exe) cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline() for extension in self.reference_extensions: index_file = self.reference_file + "." + extension self.assertTrue(os.path.exists(index_file), "Index File %s not found" % (index_file)) self.assertTrue(stdout.startswith("[bwt_gen]"), "FASTA indexing failed:\n%s\nStdout:%s" % (cmdline, stdout))
def test_index(self): """Test for creating index files for the reference genome fasta file""" cmdline = BwaIndexCommandline() cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline() output = stdout.startswith("[bwt_gen]") self.assertTrue(stdout.startswith("[bwt_gen]"), "FASTA indexing failed:\n%s\nStdout:%s" \ % (cmdline, stdout))
def create_fasta_index(self): """Test for generating index for fasta file. BWA requires an indexed fasta for each alignment operation. This should be called to create an index before any alignment operation. """ cmdline = BwaIndexCommandline(bwa_exe) cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline()
def test_index(self): """Test for creating index files for the reference genome fasta file""" cmdline = BwaIndexCommandline(bwa_exe) cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline() for extension in self.reference_extensions: index_file = self.reference_file + "." + extension self.assertTrue(os.path.exists(index_file), "Index File %s not found" % (index_file)) self.assertTrue( stdout.startswith("[bwt_gen]"), "FASTA indexing failed:\n%s\nStdout:%s" % (cmdline, stdout))
def test_index(self): """Test for creating index files for the reference genome fasta file.""" cmdline = BwaIndexCommandline(bwa_exe) cmdline.set_parameter("infile", self.reference_file) cmdline.set_parameter("algorithm", "bwtsw") stdout, stderr = cmdline() for extension in self.reference_extensions: index_file = self.reference_file + "." + extension self.assertTrue( os.path.exists(index_file), f"Index File {index_file} not found" ) self.assertIn( "Finished constructing BWT", str(stdout) + str(stderr), f"FASTA indexing failed:\n{cmdline}\nStdout:{stdout}\nStderr:{stderr}\n", )