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#!/usr/bin/env python
import os
import logging
import subprocess
class BowtieSuite(object):
def __init__(self,bt_path=''):
curr_path = os.path.realpath(bt_path)
self.bowtie_bin = os.path.join(curr_path,'bowtie')
self.bowtie_build = os.path.join(curr_path,'bowtie-build')
self.bowtie_inspect = os.path.join(curr_path,'bowtie-inspect')
def run(self, *args):
cmd = self.bowtie_bin + " " + " ".join([i for i in args])
return(subprocess.call(cmd,shell=True))
def silent_run(self, *args):
cmd = self.bowtie_bin + " " + " ".join([i for i in args])
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]))
ret = subprocess.check_call(cmd,shell=True)
os.chdir(curr_dir)
return(ret)
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