def run_bowtie2(reads, reference, outfile, threads=1):
assert is_bowtie2_indexed(reference)
cmd = ' '.join([
'bowtie2',
'-x', reference,
'-U', reads,
'-f', # reads are in fasta format
'--end-to-end --very-fast',
'--threads', str(threads),
'--all', # report all alignments
'--reorder', # force SAM output order to match order of input reads
'-S', outfile # output in SAM format
])
common.syscall(cmd)
def _run_primer3_core(self, fasta_file, config_file, outfile):
tmpdir = tempfile.mkdtemp(prefix='tmp.run_primer3_core.',
dir=os.getcwd())
boulder_file = os.path.join(tmpdir, 'in.boulder')
pyfastaq.tasks.to_boulderio(self.input_fasta, boulder_file)
cmd = ' '.join([
self.primer3_command,
'-p3_settings_file=' + self.config_file,
'<',
boulder_file,
'| gzip -9 -c >',
outfile,
])
common.syscall(cmd)
shutil.rmtree(tmpdir)
def _run_primer3_core(self, fasta_file, config_file, outfile):
tmpdir = tempfile.mkdtemp(prefix="tmp.run_primer3_core.", dir=os.getcwd())
boulder_file = os.path.join(tmpdir, "in.boulder")
pyfastaq.tasks.to_boulderio(self.input_fasta, boulder_file)
cmd = " ".join(
[
self.primer3_command,
"-p3_settings_file=" + self.config_file,
"<",
boulder_file,
"| gzip -9 -c >",
outfile,
]
)
common.syscall(cmd)
shutil.rmtree(tmpdir)
def run_bowtie2(reads, reference, outfile, threads=1):
assert is_bowtie2_indexed(reference)
cmd = ' '.join([
'bowtie2',
'-x',
reference,
'-U',
reads,
'-f', # reads are in fasta format
'--end-to-end --very-fast',
'--threads',
str(threads),
'--all', # report all alignments
'--reorder', # force SAM output order to match order of input reads
'-S',
outfile # output in SAM format
])
common.syscall(cmd)
def bowtie2_index(infile, outprefix=None):
if outprefix is None:
outprefix = infile
if not is_bowtie2_indexed(infile):
common.syscall('bowtie2-build ' + infile + ' ' + outprefix)
def bowtie2_index(infile, outprefix=None):
if outprefix is None:
outprefix = infile
if not is_bowtie2_indexed(infile):
common.syscall('bowtie2-build ' + infile + ' ' + outprefix)