/tools/peak_calling/ccat_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 41 lines · 35 code · 6 blank · 0 comment · 6 complexity · 2e2d7f62f405275c5b17be597e76d561 MD5 · raw file
- import sys, subprocess, tempfile, shutil, os.path
- CCAT_BINARY = "CCAT"
- def get_top_count( filename ):
- for line in open( filename ):
- if line.startswith( 'outputNum' ):
- return int( line.split()[-1].strip() )
- def stop_err( tmp_dir, exception ):
- print >> sys.stderr, "Error running CCAT."
- shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
- raise exception
- def main():
- input_tag_file = sys.argv[1]
- input_control_file = sys.argv[2]
- chrom_info_file = sys.argv[3]
- input_config_file = sys.argv[4]
- project_name = sys.argv[5]
- output_peak_file = sys.argv[6]
- output_region_file = sys.argv[7]
- output_top_file = sys.argv[8]
- output_log_file = sys.argv[9]
-
- tmp_dir = tempfile.mkdtemp()
- try:
- assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist."
- proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
- proc.wait()
- if proc.returncode:
- raise Exception( "Error code: %i" % proc.returncode )
- output_num = get_top_count( input_config_file )
- shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
- shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
- shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
- except Exception, e:
- return stop_err( tmp_dir, e )
- os.rmdir( tmp_dir ) #clean up empty temp working directory
- if __name__ == "__main__": main()