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comparison glimmer3_wrapper.py @ 0:9c8ffce71f7c draft default tip

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author crs4
date Mon, 09 Sep 2013 12:16:17 -0400
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-1:000000000000 0:9c8ffce71f7c
1 # -*- coding: utf-8 -*-
2 """
3 Glimmer --> glimmer3
4 version 0.2 (andrea.pinna@crs4.it)
5 """
6
7 import optparse
8 import shutil
9 import subprocess
10 import sys
11
12 def __main__():
13 # load arguments
14 print 'Parsing input options...'
15 parser = optparse.OptionParser()
16 parser.add_option('--glSequence', dest='sequence', help='')
17 parser.add_option('--glIcm', dest='icm', help='')
18 #parser.add_option('--glPrefix', dest='prefix', help='')
19 parser.add_option('--glStartCodons', dest='start_codons', help='')
20 parser.add_option('--glRbsPwm', dest='rbs_pwm', help='')
21 parser.add_option('--glGcPercent', dest='gc_percent', type='float', help='')
22 parser.add_option('--glEntropy', dest='entropy', help='')
23 parser.add_option('--glFirstCodon', action='store_true', dest='first_codon', help='')
24 parser.add_option('--glGeneLen', dest='gene_len', type='int', help='')
25 parser.add_option('--glIgnore', dest='ignore', help='')
26 parser.add_option('--glLinear', action='store_true', dest='linear', help='')
27 parser.add_option('--glOrfCoords', dest='orf_coords', help='')
28 parser.add_option('--glSeparateGenes', action='store_true', dest='separate_genes', help='')
29 parser.add_option('--glMaxOverlap', dest='max_olap', type='int', help='')
30 parser.add_option('--glStartProbs', dest='start_probs', help='')
31 parser.add_option('--glIgnoreScoreLen', dest='ignore_score_len', type='int', help='')
32 parser.add_option('--glNoIndep', action='store_true', dest='no_indep', help='')
33 parser.add_option('--glThreshold', dest='threshold', type='int', help='')
34 parser.add_option('--glExtend', action='store_true', dest='extend', help='')
35 parser.add_option('--glTransTable', dest='trans_table', type='int', help='')
36 parser.add_option('--glStopCodons', dest='stop_codons', help='')
37 parser.add_option('--glDetail', dest='detail', help='')
38 parser.add_option('--glPredict', dest='predict', help='')
39 parser.add_option('--logfile', dest='logfile', help='')
40 (options, args) = parser.parse_args()
41 if len(args) > 0:
42 parser.error('Wrong number of arguments')
43
44 # build Glimmer3 command to be executed
45 # sequence file
46 sequence = options.sequence
47 # icm file
48 icm = options.icm
49 # prefix (not needed)
50 prefix = 'prefix'
51 # start codons
52 if options.start_codons:
53 start_codons = '--start_codons %s' % (options.start_codons)
54 else:
55 start_codons = ''
56 # rbs_pwm
57 if options.rbs_pwm:
58 rbs_pwm = '--rbs_pwm %s' % (options.rbs_pwm)
59 else:
60 rbs_pwm = ''
61 # gc percentage
62 if options.gc_percent is not None:
63 gc_percent = '--gc_percent %s' % (options.gc_percent)
64 else:
65 gc_percent = ''
66 # entropy
67 if options.entropy:
68 entropy = "--entropy '%s'" % (options.entropy)
69 else:
70 entropy = ''
71 # first_codon
72 if options.first_codon:
73 first_codon = '--first_codon'
74 else:
75 first_codon = ''
76 # gene length
77 if options.gene_len is not None:
78 gene_len = '--gene_len %d' % (options.gene_len)
79 else:
80 gene_len = ''
81 # ignore
82 if options.ignore:
83 ignore = '--ignore %s' % (options.ignore)
84 else:
85 ignore = ''
86 # linear
87 if options.linear:
88 linear = '--linear'
89 else:
90 linear = ''
91 # orf_coords
92 if options.orf_coords:
93 orf_coords = '--orf_coords %s' % (options.orf_coords)
94 else:
95 orf_coords = ''
96 # separate genes
97 if options.separate_genes:
98 separate_genes = '--separate_genes'
99 else:
100 separate_genes = ''
101 # max overlap
102 if options.max_olap is not None:
103 max_olap = '--max_olap %d' % (options.max_olap)
104 else:
105 max_olap = ''
106 # start probs
107 if options.start_probs:
108 start_probs = '--start_probs %s' % (options.start_probs)
109 else:
110 start_probs = ''
111 # ignore score length
112 if options.ignore_score_len is not None:
113 ignore_score_len = '--ignore_score_len %d' % (options.ignore_score_len)
114 else:
115 ignore_score_len = ''
116 # no indep
117 if options.no_indep:
118 no_indep = '--no_indep'
119 else:
120 no_indep = ''
121 # threshold
122 if options.threshold is not None:
123 threshold = '--threshold %d' % (options.threshold)
124 else:
125 threshold = ''
126 # extend
127 if options.extend:
128 extend = '--extend'
129 else:
130 extend = ''
131 # trans table
132 if options.trans_table is not None:
133 trans_table = '--trans_table %d' % (options.trans_table)
134 else:
135 trans_table = ''
136 # stop codons
137 if options.stop_codons:
138 stop_codons = '--stop_codons %s' % (options.stop_codons)
139 else:
140 stop_codons = ''
141 logfile = options.logfile
142
143 # Build Glimmer3 command
144 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)
145 print '\nGlimmer3 command to be executed: \n %s' % (cmd)
146
147 print 'Executing Glimmer3...'
148 if logfile:
149 log = open(logfile, 'w')
150 else:
151 log = sys.stdout
152 try:
153 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
154 finally:
155 if log != sys.stdout:
156 log.close()
157 print 'Glimmer3 executed!'
158
159 shutil.move(prefix + ".detail", options.detail)
160 shutil.move(prefix + ".predict", options.predict)
161
162
163 if __name__ == "__main__":
164 __main__()