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",
)
