--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/extract/phastOdds/get_scores_galaxy.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,147 @@
+#!/usr/bin/env python
+
+"""
+usage: %prog data_file.h5 region_mapping.bed in_file out_file chrom_col start_col end_col [options]
+   -p, --perCol: standardize to lod per column
+"""
+
+from __future__ import division
+
+import sys
+from galaxy import eggs
+from numpy import *
+from tables import *
+
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+from bx import intervals
+
+# ignore wanrnings about NumArray flavor
+from warnings import filterwarnings
+from tables.exceptions import FlavorWarning
+filterwarnings("ignore", category=FlavorWarning)
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def main():
+    # Parse command line
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        h5_fname = args[0]
+        mapping_fname = args[1]
+        in_fname = args[2]
+        out_fname = args[3]
+        chrom_col, start_col, end_col = map( lambda x: int( x ) - 1, args[4:7] )
+        per_col = bool( options.perCol )
+    except Exception, e:
+        doc_optparse.exception()
+        
+    if h5_fname == 'None.h5':
+        stop_err( 'Invalid genome build, this tool currently only works with data from build hg17.  Click the pencil icon in your history item to correct the build if appropriate.' )
+        
+    # Open the h5 file
+    h5 = openFile( h5_fname, mode = "r" )
+    # Load intervals and names for the subregions
+    intersecters = {}
+    for i, line in enumerate( file( mapping_fname ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            chr, start, end, name = line.split()[0:4]
+            if not intersecters.has_key( chr ): 
+                intersecters[ chr ] = intervals.Intersecter()
+            intersecters[ chr ].add_interval( intervals.Interval( int( start ), int( end ), name ) )
+
+    # Find the subregion containing each input interval
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_line = ''
+    out_file = open( out_fname, "w" )
+    warnings = []
+    warning = ''
+    for i, line in enumerate( file( in_fname ) ):
+        line = line.rstrip( '\r\n' )
+        if line.startswith( '#' ):
+            if i == 0:
+                out_file.write( "%s\tscore\n" % line )
+            else:
+                out_file.write( "%s\n" % line )
+        fields = line.split( "\t" )
+        try:
+            chr = fields[ chrom_col ]
+            start = int( fields[ start_col ] )
+            end = int( fields[ end_col ] )
+        except:
+            warning = "Invalid value for chrom, start or end column."
+            warnings.append( warning )
+            skipped_lines += 1
+            if not invalid_line:
+                first_invalid_line = i + 1
+                invalid_line = line
+            continue
+        # Find matching interval
+        try:
+            matches = intersecters[ chr ].find( start, end )
+        except:
+            warning = "'%s' is not a valid chrom value for the region. " %chr
+            warnings.append( warning )
+            skipped_lines += 1
+            if not invalid_line:
+                first_invalid_line = i + 1
+                invalid_line = line
+            continue
+        if not len( matches ) == 1:
+            warning = "Interval must match exactly one target region. "
+            warnings.append( warning )
+            skipped_lines += 1
+            if not invalid_line:
+                first_invalid_line = i + 1
+                invalid_line = line
+            continue
+        region = matches[0]
+        if not ( start >= region.start and end <= region.end ):
+            warning = "Interval must fall entirely within region. "
+            warnings.append( warning )
+            skipped_lines += 1
+            if not invalid_line:
+                first_invalid_line = i + 1
+                invalid_line = line
+            continue
+        region_name = region.value
+        rel_start = start - region.start
+        rel_end = end - region.start
+        if not rel_start < rel_end:
+            warning = "Region %s is empty, relative start:%d, relative end:%d. " % ( region_name, rel_start, rel_end )
+            warnings.append( warning )
+            skipped_lines += 1
+            if not invalid_line:
+                first_invalid_line = i + 1
+                invalid_line = line
+            continue
+        s = h5.getNode( h5.root, "scores_" + region_name )
+        c = h5.getNode( h5.root, "counts_" + region_name )
+        score = s[rel_end-1]
+        count = c[rel_end-1]
+        if rel_start > 0:
+            score -= s[rel_start-1]
+            count -= c[rel_start-1]
+        if per_col: 
+            score /= count
+        fields.append( str( score ) )
+        out_file.write( "%s\n" % "\t".join( fields ) )
+    # Close the file handle
+    h5.close()
+    out_file.close()
+
+    if warnings:
+        warn_msg = "PhastOdds scores are only available for ENCODE regions. %d warnings, 1st is: " % len( warnings )
+        warn_msg += warnings[0]
+        print warn_msg
+    if skipped_lines:
+        print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+
+if __name__ == "__main__": main()