Mercurial > repos > vipints > fml_mergeloci
view 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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#!/usr/bin/env python # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society # Copyright (C) 2010 Max Planck Society # # Description : Provide available source, feature types from a GFF file import re, sys import time import collections def available_limits(gff_handle): """Figure out the available feature types from the given GFF file""" filter_info = dict(gff_id = [0], gff_source_type = [1, 2], gff_source = [1], gff_type = [2]) cur_limits = dict() for filter_key in filter_info.keys(): cur_limits[filter_key] = collections.defaultdict(int) for line in gff_handle: if line.strip('\n\r')[0] != "#": parts = [p.strip() for p in line.split('\t')] if len(parts) == 1 and re.search(r'\w+', parts[0]):continue ## GFF files with FASTA sequence together assert len(parts) == 9, line for filter_key, cur_indexes in filter_info.items(): cur_id = tuple([parts[i] for i in cur_indexes]) cur_limits[filter_key][cur_id] += 1 # get rid of the default dicts final_dict = dict() for key, value_dict in cur_limits.items(): if len(key) == 1: key = key[0] final_dict[key] = dict(value_dict) return final_dict if __name__=='__main__': stime = time.asctime( time.localtime(time.time()) ) print '-------------------------------------------------------' print 'FeatureScan started on ' + stime print '-------------------------------------------------------' try: gff_handle = open(sys.argv[1], 'rU') except: sys.stderr.write("Can't open the GFF3 file, terminating...\n") sys.stderr.write("USAGE: gff_available_limits.py <gff file>\n") sys.exit(-1) final_dict = available_limits(gff_handle) gff_handle.close() print print "==Overview of available source(s) and feature type(s) from GFF file==" print print "Chromosome identifier(s) and corresponding count:" for contig, cnt in sorted(final_dict['gff_id'].items()): print '\t' + str(contig[0]) + '\t' + str(cnt) print print "Source(s) of feature and corresponding count:" for source, cnt in sorted(final_dict['gff_source'].items()): print '\t' + str(source[0]) + '\t' + str(cnt) print print "Feature type(s) and corresponding count:" for ftype, cnt in sorted(final_dict['gff_type'].items()): print '\t' + str(cnt) + '\t' + str(ftype[0]) print print "Unique combination of Feature type(s), Source(s) and corresponding count:" for sftype, cnt in sorted(final_dict['gff_source_type'].items()): print '\t' + str(cnt) + '\t' + str(sftype[0]) + ', '+ str(sftype[1]) print stime = time.asctime( time.localtime(time.time()) ) print '-------------------------------------------------------' print 'FeatureScan finished at ' + stime print '-------------------------------------------------------'