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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 #%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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4 import sys, random
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5 from copy import deepcopy
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6 from galaxy import eggs
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7 import pkg_resources
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8 pkg_resources.require( "bx-python" )
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9 import bx.intervals.io
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10 import bx.intervals.intersection
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11 import psyco_full
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12
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13 assert sys.version_info[:2] >= ( 2, 4 )
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14
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15 max_iters = 5
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16
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17 def stop_err( msg ):
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18 sys.stderr.write( msg )
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19 sys.exit()
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20
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21 #Try to add a random region
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22 def add_random_region( mimic_region, bound, exist_regions, plus_mask, minus_mask, overlaps ):
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23 region_length, region_strand = mimic_region
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24 plus_count = plus_mask.count_range()
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25 minus_count = minus_mask.count_range()
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26 gaps = []
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27
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28 if region_strand == "-":
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29 gaps = minus_mask.get_gaps( region_length )
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30 else:
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31 gaps = plus_mask.get_gaps( region_length )
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32
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33 while True:
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34 try:
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35 gap_length, gap_start, gap_end = gaps.pop( random.randint( 0, len( gaps ) - 1 ) )
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36 except:
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37 break
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38 try:
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39 start = random.randint( bound.start + gap_start, bound.start + gap_end - region_length - 1 )
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40 except ValueError, ve:
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41 stop_err( "Exception thrown generating random start value: %s" %str( ve ) )
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42
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43 end = start + region_length
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44 try_plus_mask = plus_mask.copy()
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45 try_minus_mask = minus_mask.copy()
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46
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47 if region_strand == "-":
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48 try_minus_mask.set_range( start - bound.start, end - bound.start )
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49 else:
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50 try_plus_mask.set_range( start - bound.start, end - bound.start )
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51
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52 rand_region = bx.intervals.io.GenomicInterval( None, [bound.chrom, start, end, region_strand], 0, 1, 2, 3, "+", fix_strand=True )
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53
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54 if try_plus_mask.count_range() == plus_count + region_length or try_minus_mask.count_range() == minus_count + region_length:
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55 if overlaps in ["strand", "all"]: #overlaps allowed across strands
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56 exist_regions.append( rand_region )
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57 if overlaps == "strand":
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58 return exist_regions, True, try_plus_mask, try_minus_mask
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59 else: #overlaps allowed everywhere
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60 return exist_regions, True, plus_mask, minus_mask
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61 else: #no overlapping anywhere
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62 exist_regions.append( rand_region )
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63 if region_strand == "-":
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64 return exist_regions, True, try_minus_mask.copy(), try_minus_mask
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65 else:
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66 return exist_regions, True, try_plus_mask, try_plus_mask.copy()
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67 return exist_regions, False, plus_mask, minus_mask
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68
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69 def main():
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70 includes_strand = False
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71 region_uid = sys.argv[1]
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72 mask_fname = sys.argv[2]
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73 intervals_fname = sys.argv[3]
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74 out_fname = sys.argv[4]
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75 try:
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76 mask_chr = int( sys.argv[5] ) - 1
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77 except:
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78 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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79 try:
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80 mask_start = int( sys.argv[6] ) - 1
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81 except:
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82 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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83 try:
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84 mask_end = int( sys.argv[7] ) - 1
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85 except:
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86 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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87 try:
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88 interval_chr = int( sys.argv[8] ) - 1
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89 except:
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90 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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91 try:
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92 interval_start = int( sys.argv[9] ) - 1
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93 except:
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94 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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95 try:
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96 interval_end = int( sys.argv[10] ) - 1
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97 except:
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98 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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99 try:
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100 interval_strand = int( sys.argv[11] ) - 1
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101 includes_strand = True
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102 except:
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103 interval_strand = -1
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104 if includes_strand:
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105 use_mask = sys.argv[12]
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106 overlaps = sys.argv[13]
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107 else:
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108 use_mask = sys.argv[11]
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109 overlaps = sys.argv[12]
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110 available_regions = {}
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111 loc_file = "%s/regions.loc" % sys.argv[-1]
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112
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113 for i, line in enumerate( file( loc_file ) ):
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114 line = line.rstrip( '\r\n' )
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115 if line and not line.startswith( '#' ):
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116 fields = line.split( '\t' )
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117 #read each line, if not enough fields, go to next line
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118 try:
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119 build = fields[0]
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120 uid = fields[1]
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121 description = fields[2]
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122 filepath = fields[3]
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123 available_regions[uid] = filepath
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124 except:
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125 continue
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126
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127 if region_uid not in available_regions:
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128 stop_err( "Region '%s' is invalid." % region_uid )
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129 region_fname = available_regions[region_uid].strip()
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130
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131 #set up bounding regions to hold random intervals
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132 bounds = []
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133 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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134 bounds.append( bound )
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135 #set up length and number of regions to mimic
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136 regions = [ [] for i in range( len( bounds ) ) ]
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137
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138 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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139 #loop through bounds, find first proper bounds then add
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140 #if an interval crosses bounds, it will be added to the first bound
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141 for i in range( len( bounds ) ):
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142 if bounds[i].chrom != region.chrom:
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143 continue
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144 intersecter = bx.intervals.intersection.Intersecter()
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145 intersecter.add_interval( bounds[i] )
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146 if len( intersecter.find( region.start, region.end ) ) > 0:
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147 regions[i].append( ( region.end - region.start, region.strand ) ) #add region to proper bound and go to next region
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148 break
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149 for region in regions:
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150 region.sort()
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151 region.reverse()
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152
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153 #read mask file
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154 mask = []
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155 if use_mask != "no_mask":
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156 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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157 mask.append( region )
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158
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159 try:
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160 out_file = open ( out_fname, "w" )
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161 except:
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162 stop_err( "Error opening output file '%s'." % out_fname )
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163
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164 i = 0
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165 i_iters = 0
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166 region_count = 0
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167 best_regions = []
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168 num_fail = 0
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169 while i < len( bounds ):
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170 i_iters += 1
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171 #order regions to mimic
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172 regions_to_mimic = regions[i][0:]
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173 if len( regions_to_mimic ) < 1: #if no regions to mimic, skip
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174 i += 1
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175 i_iters = 0
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176 continue
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177 #set up region mask
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178 plus_mask = Region( bounds[i].end - bounds[i].start )
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179 for region in mask:
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180 if region.chrom != bounds[i].chrom: continue
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181 mask_start = region.start - bounds[i].start
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182 mask_end = region.end - bounds[i].start
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183 if mask_start >= 0 and mask_end > 0:
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184 plus_mask.set_range( mask_start, mask_end )
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185 minus_mask = plus_mask.copy()
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186 random_regions = []
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187 num_added = 0
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188 for j in range( len( regions[i] ) ):
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189 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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190 if added:
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191 num_added += 1
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192 if num_added == len( regions_to_mimic ) or i_iters >= max_iters:
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193 if len( best_regions ) > len( random_regions ):
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194 random_regions = best_regions.copy()
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195 num_fail += ( len( regions_to_mimic ) - len( random_regions ) )
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196 i_iters = 0
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197 best_regions = []
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198 for region in random_regions:
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199 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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200 region_count += 1
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201 else:
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202 i -= 1
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203 if len( best_regions ) < len( random_regions ):
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204 best_regions = random_regions[:]
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205 i+=1
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206
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207 out_file.close()
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208 if num_fail:
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209 print "After %i iterations, %i regions could not be added." % (max_iters, num_fail)
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210 if use_mask == "use_mask":
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211 print "The mask you have provided may be too restrictive."
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212
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213 class Region( list ):
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214 """
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215 A list for on/off regions
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216 """
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217 def __init__( self, size=0 ):
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218 for i in range( size ):
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219 self.append( False )
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220 def copy( self ):
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221 return deepcopy( self )
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222 def set_range( self, start=0, end=None ):
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223 if start < 0:
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224 start = 0
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225 if ( not end and end != 0 ) or end > len( self ):
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226 end = len( self )
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227 for i in range( start, end ):
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228 self[i]=True
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229 def count_range( self, start=0, end=None ):
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230 if start < 0:
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231 start = 0
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232 if ( not end and end != 0 ) or end > len( self ):
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233 end = len( self )
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234 return self[start:end].count( True )
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235 def get_gaps( self, min_size = 0 ):
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236 gaps = []
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237 start = end = 0
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238 while True:
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239 try:
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240 start = self[end:].index( False ) + end
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241 except:
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242 break
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243 try:
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244 end = self[start:].index( True ) + start
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245 except:
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246 end = len( self )
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247 if end > start and end - start >= min_size:
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248 gaps.append( ( end - start, start, end ) )
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249 gaps.sort()
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250 gaps.reverse()
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251 return gaps
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252
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253 if __name__ == "__main__": main()
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