root/galaxy-central/tools/maf/maf_stats.py

リビジョン 2, 4.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2#Dan Blankenberg
3"""
4Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
5"""
6
7import sys
8from galaxy import eggs
9import pkg_resources; pkg_resources.require( "bx-python" )
10import bx.intervals.io
11from bx.bitset import BitSet
12from galaxy.tools.util import maf_utilities
13
14assert sys.version_info[:2] >= ( 2, 4 )
15
16def __main__():
17    maf_source_type = sys.argv.pop( 1 )
18    input_maf_filename = sys.argv[1].strip()
19    input_interval_filename = sys.argv[2].strip()
20    output_filename = sys.argv[3].strip()
21    dbkey = sys.argv[4].strip()
22    try:
23        chr_col  = int( sys.argv[5].strip() ) - 1
24        start_col = int( sys.argv[6].strip() ) - 1
25        end_col = int( sys.argv[7].strip() ) - 1
26    except:
27        print >>sys.stderr, "You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file."
28        sys.exit()
29    summary = sys.argv[8].strip()
30    if summary.lower() == "true": summary = True
31    else: summary = False
32
33    mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
34    try:
35        maf_index_filename = sys.argv[10].strip()
36    except:
37        maf_index_filename = None
38    index = index_filename = None
39    if maf_source_type == "user":
40        #index maf for use here
41        index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
42        if index is None:
43            print >>sys.stderr, "Your MAF file appears to be malformed."
44            sys.exit()
45    elif maf_source_type == "cached":
46        #access existing indexes
47        index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
48        if index is None:
49            print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
50            sys.exit()
51    else:
52        print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
53        sys.exit()
54       
55    out = open(output_filename, 'w')
56   
57    num_region = None
58    species_summary = {}
59    total_length = 0
60    #loop through interval file
61    for num_region, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_interval_filename, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ) ):
62        src = "%s.%s" % ( dbkey, region.chrom )
63        region_length = region.end - region.start
64        total_length += region_length
65        coverage = { dbkey: BitSet( region_length ) }
66       
67       
68        for block in index.get_as_iterator( src, region.start, region.end ):
69            for spec in maf_utilities.get_species_in_block( block ):
70                if spec not in coverage: coverage[spec] = BitSet( region_length )
71            for block in maf_utilities.iter_blocks_split_by_species( block ):
72                if maf_utilities.component_overlaps_region( block.get_component_by_src( src ), region ):
73                    #need to chop and orient the block
74                    block = maf_utilities.orient_block_by_region( maf_utilities.chop_block_by_region( block, src, region ), src, region, force_strand = '+' )
75                    start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start )
76                    for i in range( len( alignment[dbkey] ) ):
77                        for spec, text in alignment.items():
78                            if text[i] != '-':
79                                coverage[spec].set( start_offset + i )
80        if summary:
81            #record summary
82            for key in coverage.keys():
83                if key not in species_summary: species_summary[key] = 0
84                species_summary[key] = species_summary[key] + coverage[key].count_range()
85        else:
86            #print coverage for interval
87            coverage_sum = coverage[dbkey].count_range()
88            out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
89            keys = coverage.keys()
90            keys.remove( dbkey )
91            keys.sort()
92            for key in keys:
93                coverage_sum = coverage[key].count_range()
94                out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), key, coverage_sum, region_length - coverage_sum ) )
95    if summary:
96        out.write( "#species\tnucleotides\tcoverage\n" )
97        for spec in species_summary:
98            out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
99    out.close()
100    if num_region is not None:
101        print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length )
102    maf_utilities.remove_temp_index_file( index_filename )
103
104if __name__ == "__main__": __main__()
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