Mercurial > repos > devteam > ccat
view ccat_wrapper.py @ 1:bbfd1fbff28a draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:14:19 -0400 |
parents | 2534ec7b3d4f |
children |
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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()