/tools/maf/maf_stats.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 110 lines · 90 code · 9 blank · 11 comment · 29 complexity · fd1069da7e6fd3dc809ae4343f843f6b MD5 · raw file
- #!/usr/bin/env python
- #Dan Blankenberg
- """
- Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
- """
- import sys
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- import bx.intervals.io
- from bx.bitset import BitSet
- from galaxy.tools.util import maf_utilities
- assert sys.version_info[:2] >= ( 2, 4 )
- def __main__():
- maf_source_type = sys.argv.pop( 1 )
- input_maf_filename = sys.argv[1].strip()
- input_interval_filename = sys.argv[2].strip()
- output_filename = sys.argv[3].strip()
- dbkey = sys.argv[4].strip()
- try:
- chr_col = int( sys.argv[5].strip() ) - 1
- start_col = int( sys.argv[6].strip() ) - 1
- end_col = int( sys.argv[7].strip() ) - 1
- except:
- 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."
- sys.exit()
- summary = sys.argv[8].strip()
- if summary.lower() == "true": summary = True
- else: summary = False
- mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
- try:
- maf_index_filename = sys.argv[10].strip()
- except:
- maf_index_filename = None
- index = index_filename = None
- if maf_source_type == "user":
- #index maf for use here
- index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
- if index is None:
- print >>sys.stderr, "Your MAF file appears to be malformed."
- sys.exit()
- elif maf_source_type == "cached":
- #access existing indexes
- index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
- if index is None:
- print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
- sys.exit()
- else:
- print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
- sys.exit()
-
- out = open(output_filename, 'w')
-
- num_region = None
- num_bad_region = 0
- species_summary = {}
- total_length = 0
- #loop through interval file
- 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 ) ):
- src = "%s.%s" % ( dbkey, region.chrom )
- region_length = region.end - region.start
- if region_length < 1:
- num_bad_region += 1
- continue
- total_length += region_length
- coverage = { dbkey: BitSet( region_length ) }
-
-
- for block in index.get_as_iterator( src, region.start, region.end ):
- for spec in maf_utilities.get_species_in_block( block ):
- if spec not in coverage: coverage[spec] = BitSet( region_length )
- for block in maf_utilities.iter_blocks_split_by_species( block ):
- if maf_utilities.component_overlaps_region( block.get_component_by_src( src ), region ):
- #need to chop and orient the block
- block = maf_utilities.orient_block_by_region( maf_utilities.chop_block_by_region( block, src, region ), src, region, force_strand = '+' )
- start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start )
- for i in range( len( alignment[dbkey] ) ):
- for spec, text in alignment.items():
- if text[i] != '-':
- coverage[spec].set( start_offset + i )
- if summary:
- #record summary
- for key in coverage.keys():
- if key not in species_summary: species_summary[key] = 0
- species_summary[key] = species_summary[key] + coverage[key].count_range()
- else:
- #print coverage for interval
- coverage_sum = coverage[dbkey].count_range()
- out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
- keys = coverage.keys()
- keys.remove( dbkey )
- keys.sort()
- for key in keys:
- coverage_sum = coverage[key].count_range()
- out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), key, coverage_sum, region_length - coverage_sum ) )
- if summary:
- out.write( "#species\tnucleotides\tcoverage\n" )
- for spec in species_summary:
- out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
- out.close()
- if num_region is not None:
- print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length )
- if num_bad_region:
- print "%i regions were invalid." % ( num_bad_region )
- maf_utilities.remove_temp_index_file( index_filename )
- if __name__ == "__main__": __main__()