def test_sampe(self):
"""Test for generating samfile by paired end sequencing"""
##Generate sai files from paired end data
self.do_aln(self.infile1, self.saifile1)
self.do_aln(self.infile2, self.saifile2)
cmdline = BwaSampeCommandline()
cmdline.set_parameter("reference", self.reference_file)
cmdline.set_parameter("sai_file1", self.saifile1)
cmdline.set_parameter("sai_file2", self.saifile2)
cmdline.set_parameter("read_file1", self.infile1)
cmdline.set_parameter("read_file2", self.infile2)
stdout, stderr = cmdline(stdout=self.samfile)
with open(self.samfile, "r") as handle:
headline = handle.readline()
self.assertTrue(headline.startswith("@SQ"),
"Error generating sam files:\n%s\nOutput starts:%s" \
% (cmdline, headline))
def test_sampe(self):
"""Test for generating samfile by paired end sequencing."""
self.create_fasta_index()
# Generate sai files from paired end data
self.do_aln(self.infile1, self.saifile1)
self.do_aln(self.infile2, self.saifile2)
cmdline = BwaSampeCommandline(bwa_exe)
cmdline.set_parameter("reference", self.reference_file)
cmdline.set_parameter("sai_file1", self.saifile1)
cmdline.set_parameter("sai_file2", self.saifile2)
cmdline.set_parameter("read_file1", self.infile1)
cmdline.set_parameter("read_file2", self.infile2)
stdout, stderr = cmdline(stdout=self.samfile)
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
headline.startswith("@SQ"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
def test_sampe(self):
"""Test for generating samfile by paired end sequencing"""
##Generate sai files from paired end data
self.do_aln(self.infile1, self.saifile1)
self.do_aln(self.infile2, self.saifile2)
cmdline = BwaSampeCommandline()
cmdline.set_parameter("reference", self.reference_file)
cmdline.set_parameter("sai_file1", self.saifile1)
cmdline.set_parameter("sai_file2", self.saifile2)
cmdline.set_parameter("read_file1", self.infile1)
cmdline.set_parameter("read_file2", self.infile2)
stdout, stderr = cmdline(stdout=self.samfile)
with open(self.samfile, "r") as handle:
headline = handle.readline()
self.assertTrue(headline.startswith("@SQ"),
"Error generating sam files:\n%s\nOutput starts:%s" \
% (cmdline, headline))