Mercurial > repos > devteam > flanking_features

annotate flanking_features.py @ 3:9f12b7e500f1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author devteam
date Mon, 13 Jun 2022 16:22:18 +0000
parents a09d13b108fd
children
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1 #!/usr/bin/env python
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2 # By: Guruprasad Ananda
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3 """
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4 Fetch closest up/downstream interval from features corresponding to every interval in primary
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5
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6 usage: %prog primary_file features_file out_file direction
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7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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9 -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
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10 -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
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11 """
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12 from __future__ import print_function
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13
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14 import fileinput
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15 import sys
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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 Comment, GenomicInterval, Header, NiceReaderWrapper
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19 from bx.intervals.operations import quicksect
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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 from utils.gff_util import convert_bed_coords_to_gff, GFFIntervalToBEDReaderWrapper
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24
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25 assert sys.version_info[:2] >= ( 2, 4 )
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26
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28 def get_closest_feature(node, direction, threshold_up, threshold_down, report_func_up, report_func_down):
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29 # direction=1 for +ve strand upstream and -ve strand downstream cases; and it is 0 for +ve strand downstream and -ve strand upstream cases
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30 # threhold_Up is equal to the interval start for +ve strand, and interval end for -ve strand
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31 # threhold_down is equal to the interval end for +ve strand, and interval start for -ve strand
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32 if direction == 1:
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33 if node.maxend <= threshold_up:
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34 if node.end == node.maxend:
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35 report_func_up(node)
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36 elif node.right and node.left:
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37 if node.right.maxend == node.maxend:
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38 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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39 elif node.left.maxend == node.maxend:
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40 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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41 elif node.right and node.right.maxend == node.maxend:
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42 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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43 elif node.left and node.left.maxend == node.maxend:
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44 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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45 elif node.minend <= threshold_up:
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46 if node.end <= threshold_up:
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47 report_func_up(node)
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48 if node.left and node.right:
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49 if node.right.minend <= threshold_up:
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50 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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51 if node.left.minend <= threshold_up:
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52 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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53 elif node.left:
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54 if node.left.minend <= threshold_up:
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55 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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56 elif node.right:
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57 if node.right.minend <= threshold_up:
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58 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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59 elif direction == 0:
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60 if node.start > threshold_down:
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61 report_func_down(node)
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62 if node.left:
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63 get_closest_feature(node.left, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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64 else:
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65 if node.right:
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66 get_closest_feature(node.right, direction, threshold_up, threshold_down, report_func_up, report_func_down)
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67
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68
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69 def proximal_region_finder(readers, region, comments=True):
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70 """
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71 Returns an iterator that yields elements of the form [ <original_interval>, <closest_feature> ].
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72 Intervals are GenomicInterval objects.
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73 """
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74 primary = readers[0]
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75 features = readers[1]
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76 either = False
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77 if region == 'Upstream':
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78 up, down = True, False
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79 elif region == 'Downstream':
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80 up, down = False, True
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81 else:
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82 up, down = True, True
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83 if region == 'Either':
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84 either = True
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85
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86 # Read features into memory:
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87 rightTree = quicksect.IntervalTree()
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88 for item in features:
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89 if type( item ) is GenomicInterval:
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90 rightTree.insert( item, features.linenum, item )
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91
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92 for interval in primary:
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93 if type( interval ) is Header:
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94 yield interval
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95 if type( interval ) is Comment and comments:
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96 yield interval
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97 elif type( interval ) == GenomicInterval:
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98 chrom = interval.chrom
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99 start = int(interval.start)
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100 end = int(interval.end)
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101 strand = interval.strand
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102 if chrom not in rightTree.chroms:
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103 continue
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104 else:
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105 root = rightTree.chroms[chrom] # root node for the chrom tree
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106 result_up = []
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107 result_down = []
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108 if (strand == '+' and up) or (strand == '-' and down):
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109 # upstream +ve strand and downstream -ve strand cases
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110 get_closest_feature(root, 1, start, None, lambda node: result_up.append( node ), None)
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111
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112 if (strand == '+' and down) or (strand == '-' and up):
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113 # downstream +ve strand and upstream -ve strand case
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114 get_closest_feature(root, 0, None, end - 1, None, lambda node: result_down.append( node ))
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115
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116 if result_up:
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117 if len(result_up) > 1: # The results_up list has a list of intervals upstream to the given interval.
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118 ends = []
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119 for n in result_up:
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120 ends.append(n.end)
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121 res_ind = ends.index(max(ends)) # fetch the index of the closest interval i.e. the interval with the max end from the results_up list
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122 else:
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123 res_ind = 0
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124 if not(either):
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125 yield [ interval, result_up[res_ind].other ]
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126
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127 if result_down:
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128 if not(either):
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129 # The last element of result_down will be the closest element to the given interval
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130 yield [ interval, result_down[-1].other ]
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131
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132 if either and (result_up or result_down):
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133 iter_val = []
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134 if result_up and result_down:
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135 if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)):
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136 iter_val = [ interval, result_up[res_ind].other ]
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137 else:
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138 # The last element of result_down will be the closest element to the given interval
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139 iter_val = [ interval, result_down[-1].other ]
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140 elif result_up:
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141 iter_val = [ interval, result_up[res_ind].other ]
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142 elif result_down:
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143 # The last element of result_down will be the closest element to the given interval
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144 iter_val = [ interval, result_down[-1].other ]
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145 yield iter_val
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146
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147
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148 def main():
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149 options, args = doc_optparse.parse( __doc__ )
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150 try:
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151 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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152 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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153 in1_gff_format = bool( options.gff1 )
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154 in2_gff_format = bool( options.gff2 )
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155 in_fname, in2_fname, out_fname, direction = args
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156 except:
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157 doc_optparse.exception()
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158
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159 # Set readers to handle either GFF or default format.
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160 if in1_gff_format:
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161 in1_reader_wrapper = GFFIntervalToBEDReaderWrapper
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162 else:
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163 in1_reader_wrapper = NiceReaderWrapper
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164 if in2_gff_format:
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165 in2_reader_wrapper = GFFIntervalToBEDReaderWrapper
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166 else:
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167 in2_reader_wrapper = NiceReaderWrapper
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168
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169 g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
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170 chrom_col=chr_col_1,
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171 start_col=start_col_1,
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172 end_col=end_col_1,
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173 strand_col=strand_col_1,
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174 fix_strand=True )
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175 g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
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176 chrom_col=chr_col_2,
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177 start_col=start_col_2,
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178 end_col=end_col_2,
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179 strand_col=strand_col_2,
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180 fix_strand=True )
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181
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182 # Find flanking features.
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183 out_file = open( out_fname, "w" )
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184 try:
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185 for result in proximal_region_finder([g1, g2], direction):
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186 if type( result ) is list:
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187 line, closest_feature = result
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188 # Need to join outputs differently depending on file types.
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189 if in1_gff_format:
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190 # Output is GFF with added attribute 'closest feature.'
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191
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192 # Invervals are in BED coordinates; need to convert to GFF.
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193 line = convert_bed_coords_to_gff( line )
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194 closest_feature = convert_bed_coords_to_gff( closest_feature )
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195
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196 # Replace double quotes with single quotes in closest feature's attributes.
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197 out_file.write( "%s closest_feature \"%s\" \n" %
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198 ( "\t".join( line.fields ),
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199 "\t".join( closest_feature.fields ).replace( "\"", "\\\"" )
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200 ) )
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201 else:
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202 # Output is BED + closest feature fields.
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203 output_line_fields = []
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204 output_line_fields.extend( line.fields )
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205 output_line_fields.extend( closest_feature.fields )
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206 out_file.write( "%s\n" % ( "\t".join( output_line_fields ) ) )
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207 else:
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208 out_file.write( "%s\n" % result )
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209 except ParseError as exc:
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210 fail( "Invalid file format: %s" % str( exc ) )
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211
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212 print("Direction: %s" % (direction))
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213 if g1.skipped > 0:
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214 print(skipped( g1, filedesc=" of 1st dataset" ))
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215 if g2.skipped > 0:
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216 print(skipped( g2, filedesc=" of 2nd dataset" ))
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217
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218
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219 if __name__ == "__main__":
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220 main()