diff tools/encode/random_intervals_no_bits.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/encode/random_intervals_no_bits.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,253 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+#%prog bounding_region_file mask_intervals_file intervals_to_mimic_file out_file mask_chr mask_start mask_end interval_chr interval_start interval_end interval_strand use_mask allow_strand_overlaps
+import sys, random
+from copy import deepcopy
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+import bx.intervals.io
+import bx.intervals.intersection
+import psyco_full
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+max_iters = 5
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+#Try to add a random region
+def add_random_region( mimic_region, bound, exist_regions, plus_mask, minus_mask, overlaps ):
+    region_length, region_strand = mimic_region
+    plus_count = plus_mask.count_range()
+    minus_count = minus_mask.count_range()
+    gaps = []
+
+    if region_strand == "-":
+        gaps = minus_mask.get_gaps( region_length )
+    else:
+        gaps = plus_mask.get_gaps( region_length )
+    
+    while True:
+        try:
+            gap_length, gap_start, gap_end = gaps.pop( random.randint( 0, len( gaps ) - 1 ) )
+        except:
+            break
+        try:
+            start = random.randint( bound.start + gap_start, bound.start + gap_end - region_length - 1 )
+        except ValueError, ve:
+            stop_err( "Exception thrown generating random start value: %s" %str( ve ) )
+
+        end = start + region_length
+        try_plus_mask = plus_mask.copy()
+        try_minus_mask = minus_mask.copy()
+        
+        if region_strand == "-":
+            try_minus_mask.set_range( start - bound.start, end - bound.start )
+        else:
+            try_plus_mask.set_range( start - bound.start, end - bound.start )
+        
+        rand_region = bx.intervals.io.GenomicInterval( None, [bound.chrom, start, end, region_strand], 0, 1, 2, 3, "+", fix_strand=True )
+        
+        if try_plus_mask.count_range() == plus_count + region_length or try_minus_mask.count_range() == minus_count + region_length:
+            if overlaps in ["strand", "all"]: #overlaps allowed across strands
+                exist_regions.append( rand_region )
+                if overlaps == "strand":
+                    return exist_regions, True, try_plus_mask, try_minus_mask
+                else: #overlaps allowed everywhere
+                    return exist_regions, True, plus_mask, minus_mask
+            else: #no overlapping anywhere
+                exist_regions.append( rand_region )
+                if region_strand == "-":
+                    return exist_regions, True, try_minus_mask.copy(), try_minus_mask
+                else: 
+                    return exist_regions, True, try_plus_mask, try_plus_mask.copy()
+    return exist_regions, False, plus_mask, minus_mask
+
+def main():
+    includes_strand = False
+    region_uid = sys.argv[1]
+    mask_fname = sys.argv[2]
+    intervals_fname = sys.argv[3]
+    out_fname = sys.argv[4]
+    try:
+        mask_chr = int( sys.argv[5] ) - 1
+    except:
+        stop_err( "'%s' is an invalid chrom column for 'Intervals to Mask' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[5] ) )
+    try:
+        mask_start = int( sys.argv[6] ) - 1
+    except:
+        stop_err( "'%s' is an invalid start column for 'Intervals to Mask' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[6] ) )
+    try:
+        mask_end = int( sys.argv[7] ) - 1
+    except:
+        stop_err( "'%s' is an invalid end column for 'Intervals to Mask' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[7] ) )
+    try:
+        interval_chr = int( sys.argv[8] ) - 1
+    except:
+        stop_err( "'%s' is an invalid chrom column for 'File to Mimick' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[8] ) )
+    try:
+        interval_start = int( sys.argv[9] ) - 1
+    except:
+        stop_err( "'%s' is an invalid start column for 'File to Mimick' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[9] ) )
+    try:
+        interval_end = int( sys.argv[10] ) - 1
+    except:
+        stop_err( "'%s' is an invalid end column for 'File to Mimick' dataset, click the pencil icon in the history item to edit column settings." % str( sys.argv[10] ) )
+    try:
+        interval_strand = int( sys.argv[11] ) - 1
+        includes_strand = True
+    except:
+        interval_strand = -1
+    if includes_strand:
+        use_mask = sys.argv[12]
+        overlaps = sys.argv[13]
+    else:
+        use_mask = sys.argv[11]
+        overlaps = sys.argv[12]
+    available_regions = {}
+    loc_file = "%s/regions.loc" % sys.argv[-1]
+    
+    for i, line in enumerate( file( loc_file ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            fields = line.split( '\t' )
+            #read each line, if not enough fields, go to next line
+            try:
+                build = fields[0]
+                uid = fields[1]
+                description = fields[2]
+                filepath = fields[3]
+                available_regions[uid] = filepath
+            except:
+                continue
+
+    if region_uid not in available_regions:
+        stop_err( "Region '%s' is invalid." % region_uid )
+    region_fname = available_regions[region_uid].strip()
+
+    #set up bounding regions to hold random intervals
+    bounds = []
+    for bound in bx.intervals.io.NiceReaderWrapper( open( region_fname, 'r' ), chrom_col=0, start_col=1, end_col=2, fix_strand=True, return_header=False, return_comments=False ):
+        bounds.append( bound )
+    #set up length and number of regions to mimic
+    regions = [ [] for i in range( len( bounds ) ) ]
+
+    for region in bx.intervals.io.NiceReaderWrapper( open( intervals_fname, 'r' ), chrom_col=interval_chr, start_col=interval_start, end_col=interval_end, strand_col=interval_strand, fix_strand=True, return_header=False, return_comments=False ):
+        #loop through bounds, find first proper bounds then add
+        #if an interval crosses bounds, it will be added to the first bound
+        for i in range( len( bounds ) ):
+            if bounds[i].chrom != region.chrom:
+                continue
+            intersecter = bx.intervals.intersection.Intersecter()
+            intersecter.add_interval( bounds[i] )
+            if len( intersecter.find( region.start, region.end ) ) > 0:
+                regions[i].append( ( region.end - region.start, region.strand ) ) #add region to proper bound and go to next region
+                break
+    for region in regions:
+        region.sort()
+        region.reverse()
+    
+    #read mask file
+    mask = []
+    if use_mask != "no_mask":
+        for region in bx.intervals.io.NiceReaderWrapper( open( mask_fname, 'r' ), chrom_col=mask_chr, start_col=mask_start, end_col=mask_end, fix_strand=True, return_header=False, return_comments=False ):
+            mask.append( region )
+
+    try:
+        out_file = open ( out_fname, "w" )
+    except:
+        stop_err( "Error opening output file '%s'." % out_fname )
+
+    i = 0
+    i_iters = 0
+    region_count = 0
+    best_regions = []
+    num_fail = 0
+    while i < len( bounds ):
+        i_iters += 1
+        #order regions to mimic
+        regions_to_mimic = regions[i][0:]
+        if len( regions_to_mimic ) < 1: #if no regions to mimic, skip
+            i += 1
+            i_iters = 0
+            continue 
+        #set up region mask
+        plus_mask = Region( bounds[i].end - bounds[i].start )
+        for region in mask:
+            if region.chrom != bounds[i].chrom: continue
+            mask_start = region.start - bounds[i].start
+            mask_end = region.end - bounds[i].start
+            if mask_start >= 0 and mask_end > 0:
+                plus_mask.set_range( mask_start, mask_end )
+        minus_mask = plus_mask.copy()
+        random_regions = []
+        num_added = 0
+        for j in range( len( regions[i] ) ):
+            random_regions, added, plus_mask, minus_mask = add_random_region( regions_to_mimic[j], bounds[i], random_regions, plus_mask, minus_mask, overlaps )
+            if added: 
+                num_added += 1
+        if num_added == len( regions_to_mimic ) or i_iters >= max_iters:
+            if len( best_regions ) > len( random_regions ):
+                random_regions = best_regions.copy()
+            num_fail += ( len( regions_to_mimic ) - len( random_regions ) )
+            i_iters = 0
+            best_regions = []
+            for region in random_regions:
+                print >>out_file, "%s\t%d\t%d\t%s\t%s\t%s" % ( region.chrom, region.start, region.end, "region_" + str( region_count ), "0", region.strand )
+                region_count += 1
+        else:
+            i -= 1
+            if len( best_regions ) < len( random_regions ):
+                best_regions = random_regions[:]
+        i+=1
+    
+    out_file.close()
+    if num_fail:
+        print "After %i iterations, %i regions could not be added." % (max_iters, num_fail)
+        if use_mask == "use_mask":
+            print "The mask you have provided may be too restrictive."
+
+class Region( list ):
+    """
+    A list for on/off regions
+    """
+    def __init__( self, size=0 ):
+        for i in range( size ):
+            self.append( False )
+    def copy( self ):
+        return deepcopy( self )
+    def set_range( self, start=0, end=None ):
+        if start < 0:
+            start = 0
+        if ( not end and end != 0 ) or end > len( self ):
+            end = len( self )
+        for i in range( start, end ):
+            self[i]=True
+    def count_range( self, start=0, end=None ):
+        if start < 0:
+            start = 0
+        if ( not end and end != 0 ) or end > len( self ):
+            end = len( self )
+        return self[start:end].count( True )
+    def get_gaps( self, min_size = 0 ):
+        gaps = []
+        start = end = 0
+        while True:
+            try: 
+                start = self[end:].index( False ) + end
+            except: 
+                break
+            try: 
+                end = self[start:].index( True ) + start
+            except:
+                end = len( self )
+            if end > start and end - start >= min_size:
+                gaps.append( ( end - start, start, end ) )
+        gaps.sort()
+        gaps.reverse()
+        return gaps
+
+if __name__ == "__main__": main()