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