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annotate gops_cluster.py @ 4:05696474ee89 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:40:19 -0400
parents 765ceb06c3e2
children
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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 """
4
05696474ee89 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 from __future__ import print_function
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13
3
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14 import fileinput
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15 import sys
4
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16
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17 from bx.cookbook import doc_optparse
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18 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
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19 from bx.intervals.operations.find_clusters import find_clusters
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20 from bx.tabular.io import ParseError
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21 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
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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
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26 def main():
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27 distance = 0
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28 minregions = 2
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29 output = 1
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30
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31 options, args = doc_optparse.parse( __doc__ )
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32 try:
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33 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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34 if options.distance:
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35 distance = int( options.distance )
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36 if options.overlap:
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37 distance = -1 * int( options.overlap )
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38 if options.output:
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39 output = int( options.output )
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40 if options.minregions:
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41 minregions = int( options.minregions )
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42 in_fname, out_fname = args
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43 except:
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44 doc_optparse.exception()
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45
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46 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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47 chrom_col=chr_col_1,
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48 start_col=start_col_1,
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49 end_col=end_col_1,
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50 strand_col=strand_col_1,
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51 fix_strand=True )
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52
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53 # Get the cluster tree
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54 try:
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55 clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
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56 except ParseError as exc:
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57 fail( "Invalid file format: %s" % str( exc ) )
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58
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59 f1 = open( in_fname, "r" )
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60 out_file = open( out_fname, "w" )
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61
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62 # If "merge"
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63 if output == 1:
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64 fields = ["." for x in range(max(g1.chrom_col, g1.start_col, g1.end_col) + 1)]
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65 for chrom, tree in clusters.items():
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66 for start, end, lines in tree.getregions():
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67 fields[g1.chrom_col] = chrom
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68 fields[g1.start_col] = str(start)
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69 fields[g1.end_col] = str(end)
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70 out_file.write( "%s\n" % "\t".join( fields ) )
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71
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72 # If "filtered" we preserve order of file and comments, etc.
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73 if output == 2:
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74 linenums = dict()
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75 for chrom, tree in clusters.items():
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76 for linenum in tree.getlines():
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77 linenums[linenum] = 0
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78 linenum = -1
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79 f1.seek(0)
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80 for line in f1.readlines():
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81 linenum += 1
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82 if linenum in linenums or linenum in extra:
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83 out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
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84
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85 # If "clustered" we output original intervals, but near each other (i.e. clustered)
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86 if output == 3:
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87 linenums = list()
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88 f1.seek(0)
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89 fileLines = f1.readlines()
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90 for chrom, tree in clusters.items():
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91 for linenum in tree.getlines():
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92 out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
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93
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94 # If "minimum" we output the smallest interval in each cluster
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95 if output == 4 or output == 5:
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96 linenums = list()
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97 f1.seek(0)
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98 fileLines = f1.readlines()
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99 for chrom, tree in clusters.items():
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100 for start, end, lines in tree.getregions():
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101 outsize = -1
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102 outinterval = None
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103 for line in lines:
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104 # three nested for loops?
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105 # should only execute this code once per line
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106 fileline = fileLines[line].rstrip("\n\r")
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107 try:
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108 cluster_interval = GenomicInterval( g1, fileline.split("\t"),
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109 g1.chrom_col,
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110 g1.start_col,
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111 g1.end_col,
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112 g1.strand_col,
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113 g1.default_strand,
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114 g1.fix_strand )
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115 except Exception as exc:
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116 print(str( exc ), file=sys.stderr)
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117 f1.close()
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118 sys.exit()
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119 interval_size = cluster_interval.end - cluster_interval.start
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120 if outsize == -1 or \
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121 ( outsize > interval_size and output == 4 ) or \
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122 ( outsize < interval_size and output == 5 ):
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123 outinterval = cluster_interval
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124 outsize = interval_size
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125 out_file.write( "%s\n" % outinterval )
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126
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127 f1.close()
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128 out_file.close()
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129
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130 if g1.skipped > 0:
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131 print(skipped( g1, filedesc="" ))
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132
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133
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134 if __name__ == "__main__":
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135 main()