Mercurial > repos > vipints > fml_mergeloci
comparison fml_gff_groomer/scripts/gff_available_limits.py @ 0:79726c328621 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | vipints |
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date | Tue, 07 Jun 2011 17:29:24 -0400 |
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-1:000000000000 | 0:79726c328621 |
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1 #!/usr/bin/env python | |
2 # | |
3 # This program is free software; you can redistribute it and/or modify | |
4 # it under the terms of the GNU General Public License as published by | |
5 # the Free Software Foundation; either version 3 of the License, or | |
6 # (at your option) any later version. | |
7 # | |
8 # Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society | |
9 # Copyright (C) 2010 Max Planck Society | |
10 # | |
11 # Description : Provide available source, feature types from a GFF file | |
12 | |
13 import re, sys | |
14 import time | |
15 import collections | |
16 | |
17 def available_limits(gff_handle): | |
18 """Figure out the available feature types from the given GFF file""" | |
19 | |
20 filter_info = dict(gff_id = [0], gff_source_type = [1, 2], | |
21 gff_source = [1], gff_type = [2]) | |
22 cur_limits = dict() | |
23 for filter_key in filter_info.keys(): | |
24 cur_limits[filter_key] = collections.defaultdict(int) | |
25 for line in gff_handle: | |
26 if line.strip('\n\r')[0] != "#": | |
27 parts = [p.strip() for p in line.split('\t')] | |
28 if len(parts) == 1 and re.search(r'\w+', parts[0]):continue ## GFF files with FASTA sequence together | |
29 assert len(parts) == 9, line | |
30 for filter_key, cur_indexes in filter_info.items(): | |
31 cur_id = tuple([parts[i] for i in cur_indexes]) | |
32 cur_limits[filter_key][cur_id] += 1 | |
33 # get rid of the default dicts | |
34 final_dict = dict() | |
35 for key, value_dict in cur_limits.items(): | |
36 if len(key) == 1: | |
37 key = key[0] | |
38 final_dict[key] = dict(value_dict) | |
39 | |
40 return final_dict | |
41 | |
42 if __name__=='__main__': | |
43 | |
44 stime = time.asctime( time.localtime(time.time()) ) | |
45 print '-------------------------------------------------------' | |
46 print 'FeatureScan started on ' + stime | |
47 print '-------------------------------------------------------' | |
48 | |
49 try: | |
50 gff_handle = open(sys.argv[1], 'rU') | |
51 except: | |
52 sys.stderr.write("Can't open the GFF3 file, terminating...\n") | |
53 sys.stderr.write("USAGE: gff_available_limits.py <gff file>\n") | |
54 sys.exit(-1) | |
55 final_dict = available_limits(gff_handle) | |
56 gff_handle.close() | |
57 print | |
58 print "==Overview of available source(s) and feature type(s) from GFF file==" | |
59 print | |
60 print "Chromosome identifier(s) and corresponding count:" | |
61 for contig, cnt in sorted(final_dict['gff_id'].items()): | |
62 print '\t' + str(contig[0]) + '\t' + str(cnt) | |
63 print | |
64 print "Source(s) of feature and corresponding count:" | |
65 for source, cnt in sorted(final_dict['gff_source'].items()): | |
66 print '\t' + str(source[0]) + '\t' + str(cnt) | |
67 print | |
68 print "Feature type(s) and corresponding count:" | |
69 for ftype, cnt in sorted(final_dict['gff_type'].items()): | |
70 print '\t' + str(cnt) + '\t' + str(ftype[0]) | |
71 print | |
72 print "Unique combination of Feature type(s), Source(s) and corresponding count:" | |
73 for sftype, cnt in sorted(final_dict['gff_source_type'].items()): | |
74 print '\t' + str(cnt) + '\t' + str(sftype[0]) + ', '+ str(sftype[1]) | |
75 print | |
76 stime = time.asctime( time.localtime(time.time()) ) | |
77 print '-------------------------------------------------------' | |
78 print 'FeatureScan finished at ' + stime | |
79 print '-------------------------------------------------------' |