--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_stats.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,104 @@
+#!/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
+    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
+        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 )
+    maf_utilities.remove_temp_index_file( index_filename )
+
+if __name__ == "__main__": __main__()