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 bowtie2_index(infile, outprefix=None): if outprefix is None: outprefix = infile if not is_bowtie2_indexed(infile): common.syscall('bowtie2-build ' + infile + ' ' + outprefix)