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New reports app server and 1st report showing disk usage for dataset file system - still need to mess with styles a bit.
Also fixed update_dataset_size script and delete deprecatd random_intervals code file.
This commit is contained in:
Greg Von Kuster
@@ -1,222 +0,0 @@
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#!/usr/bin/env python2.4
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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
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from __future__ import division
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys, random
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import bisect
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from bx.bitset import *
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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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def throw_random_2( lengths, mask ):
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"""
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Version of throw using gap lists (like Hiram's randomPlacement). This
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is not ready yet!!!
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"""
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# Projected version for throwing
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bits = BitSet( mask.size )
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# Use mask to find the gaps
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gaps = []
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start = end = 0
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while 1:
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start = mask.next_clear( end )
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if start == mask.size: break
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end = mask.next_set( start )
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gaps.append( ( end-start, start, end ) )
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# Sort (long regions first )
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gaps.sort()
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gaps.reverse()
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# And throw
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for length in lengths:
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max_candidate = 0
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candidate_bases = 0
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for gap in gaps:
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if gap[0] >= length:
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max_candidate += 1
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candidate_bases += ( gap[0] - length )
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else:
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break
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if max_candidate == 0:
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raise MaxtriesException( "No gap can fit region of length %d" % length )
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# Select start position
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s = random.randrange( candidate_bases )
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# Map back to region
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chosen_index = 0
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for gap in gaps:
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gap_length, gap_start, gap_end = gap
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if s > ( gap_length - length ):
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s -= ( gap_length - length )
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chosen_index += 1
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else:
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break
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# Remove the chosen gap and split
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assert ( gap_length, gap_start, gap_end ) == gaps.pop( chosen_index )
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# gap_length, gap_start, gap_end = gaps.pop( chosen_index )
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assert s >= 0
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assert gap_start + s + length <= gap_end, "Expected: %d + %d + %d == %d <= %d" % ( gap_start, s, length, gap_start + s + length, gap_end )
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gaps.reverse()
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if s > 0:
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bisect.insort( gaps, ( s, gap_start, gap_start + s ) )
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if s + length < gap_length:
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bisect.insort( gaps, ( gap_length - ( s + length ), gap_start + s + length, gap_end) )
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gaps.reverse()
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# And finally set the bits
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assert bits[gap_start + s] == 0
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assert bits.next_set( gap_start + s, gap_start+s+length ) == gap_start+s+length
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assert( gap_start + s >= 0 and gap_start + s + length <= bits.size ), "Bad interval %d %d %d %d %d" % ( gap_start, s, length, gap_start + s + length, bits.size )
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bits.set_range( gap_start + s, length )
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assert bits.count_range( 0, bits.size ) == sum( lengths )
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return bits
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def overlapping_in_bed( fname, r_chr, r_start, r_stop, chr_col, start_col, end_col ):
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rval = []
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for line in open( fname ):
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if line.startswith( "#" ) or line.startswith( "track" ):
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continue
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fields = line.split()
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try:
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chr, start, stop = fields[chr_col], int( fields[start_col] ), int( fields[end_col] )
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if chr == r_chr and start < r_stop and stop >= r_start:
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rval.append( ( chr, max( start, r_start ), min( stop, r_stop ) ) )
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except:
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continue
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return rval
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def as_bits( region_start, region_length, intervals ):
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bits = BitSet( region_length )
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for chr, start, stop in intervals:
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bits.set_range( start - region_start, stop - start )
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return bits
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def bit_clone( bits ):
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new = BitSet( bits.size )
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new.ior( bits )
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return new
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def count_overlap( bits1, bits2 ):
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b = BitSet( bits1.size )
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b |= bits1
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b &= bits2
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return b.count_range( 0, b.size )
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def interval_lengths( bits ):
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end = 0
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while 1:
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start = bits.next_set( end )
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if start == bits.size: break
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end = bits.next_clear( start )
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yield end - start
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def main():
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#region_fname = sys.argv[1]
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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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use_mask = sys.argv[11]
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available_regions = {}
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loc_file = "/depot/data2/galaxy/regions.loc"
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for i, line in enumerate( open( 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( "Invalid region '%s' selected." % region_uid )
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region_fname = available_regions[region_uid]
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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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skipped_lines = 0
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first_invalid_line = 0
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invalid_line = ''
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for line_count, line in enumerate( file( region_fname ) ):
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if line and not line.startswith( '#' ):
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try:
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# Load lengths for all intervals overlapping region
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fields = line.split()
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r_chr, r_start, r_stop = fields[0], int( fields[1] ), int( fields[2] )
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r_length = r_stop - r_start
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# Load the mask
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if use_mask == "no_mask":
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mask = []
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else:
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mask = overlapping_in_bed( mask_fname, r_chr, r_start, r_stop, mask_chr, mask_start, mask_end )
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bits_mask = as_bits( r_start, r_length, mask )
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bits_not_masked = bit_clone( bits_mask )
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bits_not_masked.invert()
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# Load the first set
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intervals1 = overlapping_in_bed( intervals_fname, r_chr, r_start, r_stop, interval_chr, interval_start, interval_end )
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bits1 = as_bits( r_start, r_length, intervals1 )
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# Intersect it with the mask
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bits1.iand( bits_not_masked )
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# Sanity checks
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if count_overlap( bits1, bits_mask ) != 0:
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stop_err( "Overlap problem, bits: %s, mask: %s" %( str( bits1 ), str( bits_mask ) ) )
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chrom = r_chr
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# For each data set
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lengths1 = list( interval_lengths( bits1 ) )
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random1 = throw_random_2( lengths1, bits_mask )
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end =0
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while 1:
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start = random1.next_set( end )
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if start == random1.size:
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break
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end = random1.next_clear( start )
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print >>out_file, "%s\t%d\t%d" % ( chrom, start, end )
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except:
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = line_count
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invalid_line = line
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continue
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out_file.close()
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if skipped_lines:
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print "Skipped %d invalid lines starting at line # %d: %s" % ( skipped_lines, first_invalid_line, invalid_line )
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if __name__ == "__main__": main()
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