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1 #!/usr/bin/env python
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2 """
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3 Cluster regions of intervals.
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4
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5 usage: %prog in_file out_file
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6 -1, --cols1=N,N,N,N: Columns for start, end, strand in file
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7 -d, --distance=N: Maximum distance between clustered intervals
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8 -v, --overlap=N: Minimum overlap require (negative distance)
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9 -m, --minregions=N: Minimum regions per cluster
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10 -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
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11 """
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12 from galaxy import eggs
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13 import pkg_resources
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14 pkg_resources.require( "bx-python" )
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15 import sys, traceback, fileinput
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16 from warnings import warn
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17 from bx.intervals import *
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18 from bx.intervals.io import *
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19 from bx.intervals.operations.find_clusters import *
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20 from bx.cookbook import doc_optparse
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21 from galaxy.tools.util.galaxyops import *
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22
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23 assert sys.version_info[:2] >= ( 2, 4 )
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24
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25 def main():
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26 distance = 0
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27 minregions = 2
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28 output = 1
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29 upstream_pad = 0
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30 downstream_pad = 0
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31
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32 options, args = doc_optparse.parse( __doc__ )
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33 try:
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34 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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35 if options.distance: distance = int( options.distance )
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36 if options.overlap: distance = -1 * int( options.overlap )
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37 if options.output: output = int( options.output )
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38 if options.minregions: minregions = int( options.minregions )
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39 in_fname, out_fname = args
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40 except:
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41 doc_optparse.exception()
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42
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43 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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44 chrom_col=chr_col_1,
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45 start_col=start_col_1,
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46 end_col=end_col_1,
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47 strand_col=strand_col_1,
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48 fix_strand=True )
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49
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50 # Get the cluster tree
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51 try:
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52 clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
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53 except ParseError, exc:
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54 fail( "Invalid file format: %s" % str( exc ) )
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55
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56 f1 = open( in_fname, "r" )
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57 out_file = open( out_fname, "w" )
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58
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59 # If "merge"
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60 if output == 1:
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61 fields = ["." for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
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62 for chrom, tree in clusters.items():
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63 for start, end, lines in tree.getregions():
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64 fields[g1.chrom_col] = chrom
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65 fields[g1.start_col] = str(start)
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66 fields[g1.end_col] = str(end)
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67 out_file.write( "%s\n" % "\t".join( fields ) )
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68
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69 # If "filtered" we preserve order of file and comments, etc.
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70 if output == 2:
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71 linenums = dict()
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72 for chrom, tree in clusters.items():
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73 for linenum in tree.getlines():
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74 linenums[linenum] = 0
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75 linenum = -1
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76 f1.seek(0)
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77 for line in f1.readlines():
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78 linenum += 1
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79 if linenum in linenums or linenum in extra:
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80 out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
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81
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82 # If "clustered" we output original intervals, but near each other (i.e. clustered)
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83 if output == 3:
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84 linenums = list()
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85 f1.seek(0)
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86 fileLines = f1.readlines()
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87 for chrom, tree in clusters.items():
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88 for linenum in tree.getlines():
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89 out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
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90
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91 # If "minimum" we output the smallest interval in each cluster
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92 if output == 4 or output == 5:
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93 linenums = list()
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94 f1.seek(0)
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95 fileLines = f1.readlines()
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96 for chrom, tree in clusters.items():
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97 regions = tree.getregions()
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98 for start, end, lines in tree.getregions():
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99 outsize = -1
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100 outinterval = None
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101 for line in lines:
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102 # three nested for loops?
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103 # should only execute this code once per line
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104 fileline = fileLines[line].rstrip("\n\r")
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105 try:
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106 cluster_interval = GenomicInterval( g1, fileline.split("\t"),
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107 g1.chrom_col,
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108 g1.start_col,
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109 g1.end_col,
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110 g1.strand_col,
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111 g1.default_strand,
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112 g1.fix_strand )
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113 except Exception, exc:
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114 print >> sys.stderr, str( exc )
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115 f1.close()
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116 sys.exit()
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117 interval_size = cluster_interval.end - cluster_interval.start
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118 if outsize == -1 or \
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119 ( outsize > interval_size and output == 4 ) or \
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120 ( outsize < interval_size and output == 5 ) :
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121 outinterval = cluster_interval
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122 outsize = interval_size
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123 out_file.write( "%s\n" % outinterval )
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124
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125 f1.close()
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126 out_file.close()
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127
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128 if g1.skipped > 0:
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129 print skipped( g1, filedesc="" )
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130
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131 if __name__ == "__main__":
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132 main()
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