diff build-icm_wrapper.py @ 0:9c8ffce71f7c draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build-icm_wrapper.py	Mon Sep 09 12:16:17 2013 -0400
@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+"""
+Glimmer --> build-icm
+version 0.2 ([e-mail])
+"""
+
+import optparse
+import subprocess
+import sys
+
+def __main__():
+    # load arguments
+    print 'Parsing Build-ICM input options...'
+    parser = optparse.OptionParser()
+    parser.add_option('--biSequence', dest='sequence', help='')
+    parser.add_option('--biDepth', dest='depth', type='int', help='')
+    parser.add_option('--biNoStops', action='store_true', dest='no_stops', help='')
+    parser.add_option('--biPeriod', dest='period', type='int', help='')
+    parser.add_option('--biReverse', action='store_true', dest='reverse', help='')
+    parser.add_option('--biWidth', dest='width', type='int', help='')
+    parser.add_option('--biTransTable', dest='trans_table', type='int', help='')
+    parser.add_option('--biStopCodons', dest='stop_codons', help='')
+    parser.add_option('--biIcm', dest='output', help='')
+    parser.add_option('--logfile', dest='logfile', help='')
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    # build Build-ICM command to be executed
+    sequence = options.sequence
+    if options.depth is not None:
+        depth = '--depth %d' % (options.depth)
+    else:
+        depth = ''
+    if options.no_stops:
+        no_stops = '--no_stops'
+    else:
+        no_stops = ''
+    if options.period is not None:
+        period = '--period %d' % (options.period)
+    else:
+        period = ''
+    if options.reverse:
+        reverse = '--reverse'
+    else:
+        reverse = ''
+    if options.width is not None:
+        width = '--width %d' % (options.width)
+    else:
+        width = ''
+    if options.trans_table is not None:
+        trans_table = '--trans_table %d' % (options.trans_table)
+    else:
+        trans_table = ''
+    if options.stop_codons:
+        stop_codons = '--stop_codons %s' % (options.stop_codons)
+    else:
+        stop_codons = ''
+    output = options.output
+    logfile = options.logfile
+    
+    # Build Build-ICM command
+    cmd = 'build-icm %s %s %s %s %s %s %s %s < %s ' % (depth, no_stops, period, reverse, width, trans_table, stop_codons, output, sequence)
+    print '\nBuild-ICM command to be executed: \n %s' % (cmd)
+    
+    print 'Executing Build-ICM...'
+    if logfile:
+        log = open(logfile, 'w')
+    else:
+        log = sys.stdout
+    try:
+        subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
+    finally:
+        if log != sys.stdout:
+            log.close()
+    print 'Build-ICM executed!'
+
+
+if __name__ == "__main__":
+    __main__()