--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer3_wrapper.py	Mon Sep 09 12:16:17 2013 -0400
@@ -0,0 +1,164 @@
+# -*- coding: utf-8 -*-
+"""
+Glimmer --> glimmer3
+version 0.2 (andrea.pinna@crs4.it)
+"""
+
+import optparse
+import shutil
+import subprocess
+import sys
+
+def __main__():
+    # load arguments
+    print 'Parsing input options...'
+    parser = optparse.OptionParser()
+    parser.add_option('--glSequence', dest='sequence', help='')
+    parser.add_option('--glIcm', dest='icm', help='')
+    #parser.add_option('--glPrefix', dest='prefix', help='')
+    parser.add_option('--glStartCodons', dest='start_codons', help='')
+    parser.add_option('--glRbsPwm', dest='rbs_pwm', help='')
+    parser.add_option('--glGcPercent', dest='gc_percent', type='float', help='')
+    parser.add_option('--glEntropy', dest='entropy', help='')
+    parser.add_option('--glFirstCodon', action='store_true', dest='first_codon', help='')
+    parser.add_option('--glGeneLen', dest='gene_len', type='int', help='')
+    parser.add_option('--glIgnore', dest='ignore', help='')
+    parser.add_option('--glLinear', action='store_true', dest='linear', help='')
+    parser.add_option('--glOrfCoords', dest='orf_coords', help='')
+    parser.add_option('--glSeparateGenes', action='store_true', dest='separate_genes', help='')
+    parser.add_option('--glMaxOverlap', dest='max_olap', type='int', help='')
+    parser.add_option('--glStartProbs', dest='start_probs', help='')
+    parser.add_option('--glIgnoreScoreLen', dest='ignore_score_len', type='int', help='')
+    parser.add_option('--glNoIndep', action='store_true', dest='no_indep', help='')
+    parser.add_option('--glThreshold', dest='threshold', type='int', help='')
+    parser.add_option('--glExtend', action='store_true', dest='extend', help='')
+    parser.add_option('--glTransTable', dest='trans_table', type='int', help='')
+    parser.add_option('--glStopCodons', dest='stop_codons', help='')
+    parser.add_option('--glDetail', dest='detail', help='')
+    parser.add_option('--glPredict', dest='predict', help='')
+    parser.add_option('--logfile', dest='logfile', help='')
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    # build Glimmer3 command to be executed
+    # sequence file
+    sequence = options.sequence
+    # icm file
+    icm = options.icm
+    # prefix (not needed)
+    prefix = 'prefix'
+    # start codons
+    if options.start_codons:
+        start_codons = '--start_codons %s' % (options.start_codons)
+    else:
+        start_codons = ''
+    # rbs_pwm
+    if options.rbs_pwm:
+        rbs_pwm = '--rbs_pwm %s' % (options.rbs_pwm)
+    else:
+        rbs_pwm = ''
+    # gc percentage
+    if options.gc_percent is not None:
+        gc_percent = '--gc_percent %s' % (options.gc_percent)
+    else:
+        gc_percent = ''
+    # entropy
+    if options.entropy:
+        entropy = "--entropy '%s'" % (options.entropy)
+    else:
+        entropy = ''
+    # first_codon
+    if options.first_codon:
+        first_codon = '--first_codon'
+    else:
+        first_codon = ''
+    # gene length
+    if options.gene_len is not None:
+        gene_len = '--gene_len %d' % (options.gene_len)
+    else:
+        gene_len = ''
+    # ignore
+    if options.ignore:
+        ignore = '--ignore %s' % (options.ignore)
+    else:
+        ignore = ''
+    # linear
+    if options.linear:
+        linear = '--linear'
+    else:
+        linear = ''
+    # orf_coords
+    if options.orf_coords:
+        orf_coords = '--orf_coords %s' % (options.orf_coords)
+    else:
+        orf_coords = ''
+    # separate genes
+    if options.separate_genes:
+        separate_genes = '--separate_genes'
+    else:
+        separate_genes = ''
+    # max overlap
+    if options.max_olap is not None:
+        max_olap = '--max_olap %d' % (options.max_olap)
+    else:
+        max_olap = ''
+    # start probs
+    if options.start_probs:
+        start_probs = '--start_probs %s' % (options.start_probs)
+    else:
+        start_probs = ''
+    # ignore score length
+    if options.ignore_score_len is not None:
+        ignore_score_len = '--ignore_score_len %d' % (options.ignore_score_len)
+    else:
+        ignore_score_len = ''
+    # no indep
+    if options.no_indep:
+        no_indep = '--no_indep'
+    else:
+        no_indep = ''
+    # threshold
+    if options.threshold is not None:
+        threshold = '--threshold %d' % (options.threshold)
+    else:
+        threshold = ''
+    # extend
+    if options.extend:
+        extend = '--extend'
+    else:
+        extend = ''
+    # trans table
+    if options.trans_table is not None:
+        trans_table = '--trans_table %d' % (options.trans_table)
+    else:
+        trans_table = ''
+    # stop codons
+    if options.stop_codons:
+        stop_codons = '--stop_codons %s' % (options.stop_codons)
+    else:
+        stop_codons = ''
+    logfile = options.logfile
+    
+    # Build Glimmer3 command
+    cmd = 'glimmer3 %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (start_codons, rbs_pwm, gc_percent, entropy, first_codon, gene_len, ignore, linear, orf_coords, separate_genes, max_olap, start_probs, ignore_score_len, no_indep, threshold, extend, trans_table, stop_codons, sequence, icm, prefix)
+    print '\nGlimmer3 command to be executed: \n %s' % (cmd)
+    
+    print 'Executing Glimmer3...'
+    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 'Glimmer3 executed!'
+    
+    shutil.move(prefix + ".detail", options.detail)
+    shutil.move(prefix + ".predict", options.predict)
+
+
+if __name__ == "__main__":
+    __main__()