[2] | 1 | #!/usr/bin/env python |
---|
| 2 | #Dan Blankenberg |
---|
| 3 | """ |
---|
| 4 | Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended. |
---|
| 5 | """ |
---|
| 6 | |
---|
| 7 | import sys |
---|
| 8 | from galaxy import eggs |
---|
| 9 | import pkg_resources; pkg_resources.require( "bx-python" ) |
---|
| 10 | import bx.intervals.io |
---|
| 11 | from bx.bitset import BitSet |
---|
| 12 | from galaxy.tools.util import maf_utilities |
---|
| 13 | |
---|
| 14 | assert sys.version_info[:2] >= ( 2, 4 ) |
---|
| 15 | |
---|
| 16 | def __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 | |
---|
| 104 | if __name__ == "__main__": __main__() |
---|