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#!/usr/bin/python3
import os
import logging
import subprocess
class BowtieSuite(object):
def __init__(self,bt2_path=''):
curr_path = os.path.realpath(bt2_path)
self.bowtie_bin = os.path.join(curr_path,'bowtie2')
self.bowtie_build = os.path.join(curr_path,'bowtie2-build')
self.bowtie_inspect = os.path.join(curr_path,'bowtie2-inspect')
logging.info('bowtie2 path: ' + self.bowtie_bin)
logging.info('bowtie2-build path: ' + self.bowtie_build)
logging.info('bowtie2-inspect path: ' + self.bowtie_inspect)
def run(self, *args):
cmd = self.bowtie_bin + " " + " ".join([i for i in args])
logging.debug('align cmd: ' + cmd)
return(subprocess.call(cmd,shell=True))
def silent_run(self, *args):
cmd = self.bowtie_bin + " " + " ".join([i for i in args])
logging.debug('align cmd (silent): ' + cmd)
return(subprocess.call(cmd,shell=True,stderr=open(os.devnull, 'w')))
def build(self, *args):
cmd = self.bowtie_build + " " + " ".join([i for i in args])
curr_dir = os.getcwd()
os.chdir(os.path.dirname(cmd.split()[-2]))
logging.debug('build cmd: ' + cmd)
ret = subprocess.check_call(cmd,shell=True)
os.chdir(curr_dir)
return(ret)
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