Mercurial > repos > devteam > mine
view mine_wrapper.py @ 1:5e2c89443c44 draft default tip
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947
author | devteam |
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date | Tue, 21 Jul 2015 15:36:05 -0400 |
parents | 783d91de9e6d |
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#!/usr/bin/env python #Dan Blankenberg """ A wrapper script for running the MINE.jar commands. """ import sys, optparse, os, tempfile, subprocess, shutil CHUNK_SIZE = 2**20 #1mb BASE_NAME = "galaxy_mime_file.txt" JOB_ID = "galaxy_mine" def cleanup_before_exit( tmp_dir ): if tmp_dir and os.path.exists( tmp_dir ): print os.listdir( tmp_dir ) shutil.rmtree( tmp_dir ) def open_file_from_option( filename, mode = 'rb' ): if filename: return open( filename, mode = mode ) return None def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' ) parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' ) parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' ) parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' ) parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' ) parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' ) parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' ) parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' ) parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' ) parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) (options, args) = parser.parse_args() tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' ) tmp_input_name = os.path.join( tmp_dir, BASE_NAME ) if options.permute: permute = "-permute" else: permute = "" os.symlink( options.infile, tmp_input_name ) cmd = 'java -jar "%s" "%s" %s -cv%s -exp%s -c%s %s "%s"' % ( options.jar, tmp_input_name, options.master_variable, options.cv, options.exp, options.c, permute, JOB_ID ) print cmd #set up stdout and stderr output options stdout = open_file_from_option( options.stdout, mode = 'wb' ) stderr = open_file_from_option( options.stderr, mode = 'wb' ) #if no stderr file is specified, we'll use our own if stderr is None: stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir ) proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) return_code = proc.wait() if return_code: stderr_target = sys.stderr else: stderr_target = sys.stdout stderr.flush() stderr.seek(0) while True: chunk = stderr.read( CHUNK_SIZE ) if chunk: stderr_target.write( chunk ) else: break stderr.close() print os.listdir( tmp_dir ) shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results ) shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log ) cleanup_before_exit( tmp_dir ) if __name__=="__main__": __main__()