def test_faidx(self):
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()
self.assertFalse(
stderr, f"Samtools faidx failed:\n{cmdline}\nStderr:{stderr}")
self.assertTrue(os.path.isfile(self.referenceindexfile))
def test_faidx(self):
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()
self.assertFalse(stderr,
"Samtools faidx failed:\n%s\nStderr:%s"
% (cmdline, stderr))
self.assertTrue(os.path.isfile(self.referenceindexfile))
def gdcs_fai(sample, analysistype='GDCS'):
"""
GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
reverse baiting
:param sample: sample object
:param analysistype: current analysis being performed
"""
from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
try:
# Find the .fai file in the target path
sample[analysistype].faifile = glob(os.path.join(sample[analysistype].targetpath, '*.fai'))[0]
except IndexError:
target_file = glob(os.path.join(sample[analysistype].targetpath, '*.fasta'))[0]
samindex = SamtoolsFaidxCommandline(reference=target_file)
map(StringIO, samindex(cwd=sample[analysistype].targetpath))
sample[analysistype].faifile = glob(os.path.join(sample[analysistype].targetpath, '*.fai'))[0]
# Get the fai file into a dictionary to be used in parsing results
try:
with open(sample[analysistype].faifile, 'r') as faifile:
for line in faifile:
data = line.split('\t')
try:
sample[analysistype].faidict[data[0]] = int(data[1])
except KeyError:
sample[analysistype].faidict = dict()
sample[analysistype].faidict[data[0]] = int(data[1])
except FileNotFoundError:
pass
def test_index_target(variables):
targetpath = os.path.join(variables.targetpath, 'bait')
target_index = SamtoolsFaidxCommandline(
reference=os.path.join(targetpath, 'baitedtargets.fa'))
target_index()
size = os.stat(os.path.join(targetpath, 'baitedtargets.fa.fai'))
assert size.st_size > 0
def create_fasta_index(self):
"""Create index for reference fasta sequence."""
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()
def create_fasta_index(self):
"""Creates index for reference fasta sequence."""
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()