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

リビジョン 2, 2.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2
3"""
4Read a maf and output intervals for specified list of species.
5"""
6import sys, os
7from galaxy import eggs
8import pkg_resources; pkg_resources.require( "bx-python" )
9from bx.align import maf
10from galaxy.tools.util import maf_utilities
11
12assert sys.version_info[:2] >= ( 2, 4 )
13
14def __main__():   
15    input_filename = sys.argv[1]
16    output_filename = sys.argv[2]
17    output_id = sys.argv[3]
18    #where to store files that become additional output
19    database_tmp_dir =  sys.argv[4]
20    primary_spec = sys.argv[5]
21    species = sys.argv[6].split( ',' )
22    all_species = sys.argv[7].split( ',' )
23    partial = sys.argv[8]
24    keep_gaps = sys.argv[9]
25    out_files = {}
26   
27    if "None" in species:
28        species = []
29   
30    if primary_spec not in species:
31        species.append( primary_spec )
32    if primary_spec not in all_species:
33        all_species.append( primary_spec )
34   
35    all_species.sort()
36    for spec in species:
37        if spec == primary_spec:
38            out_files[ spec ] = open( output_filename, 'wb+' )
39        else:
40            out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' )
41        out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) )
42    num_species = len( all_species )
43   
44    file_in = open( input_filename, 'r' )
45    maf_reader = maf.Reader( file_in )
46   
47    for i, m in enumerate( maf_reader ):
48        for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ):
49            if len( block.components ) < num_species and partial == "partial_disallowed": continue
50            sequences = {}
51            for c in block.components:
52                spec, chrom = maf_utilities.src_split( c.src )
53                if keep_gaps == 'remove_gaps':
54                    sequences[ spec ] = c.text.replace( '-', '' )
55                else:
56                    sequences[ spec ] = c.text
57            sequences = '\t'.join( [ sequences.get( spec, '' ) for spec in all_species ] )
58            for spec in species:
59                c = block.get_component_by_src_start( spec )
60                if c is not None:
61                    spec2, chrom = maf_utilities.src_split( c.src )
62                    assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) )
63                    out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) )
64    file_in.close()
65    for file_out in out_files.values():
66        file_out.close()
67
68if __name__ == "__main__": __main__()
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