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1 #!/project/bioperl/perl-5.10.1-sles11/bin/perl -w
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2 #
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3 #------------------------------------------------------------------------------
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4 # University of Minnesota
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5 # Copyright 2010, Regents of the University of Minnesota
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6 #------------------------------------------------------------------------------
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7 # Author:
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8 #
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9 # Jesse Erdmann
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10 #
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11 # POD documentation
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12 #------------------------------------------------------------------------------
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13 =pod BEGIN
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14
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15 =head1 NAME
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16
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17 feature_finder.pl - find features nearest to another set of features within a given window.
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18
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19 =head1 SYNOPSIS
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20
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21 feature_finder.pl [-help] [-intervals interval_file] [-icol interval_column_config]
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22 [-features feature_file] [-fcol feature_column_config]
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23 [-results ALL|CLOSEST] [-direction BOTH|EITHER|UPSTREAM|DOWNSTREAM]
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24 [-window win_size] [-output output_file] [-html html_output_file]
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25 [-db db_name] [-cturl custom_track_url] [-include_capture]
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26 [-promoter PROMOTER_BP]
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27
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28 =head1 OPTIONS
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29
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30 =over 6
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31
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32 =item B<-help>
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33
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34 Print a usage summary
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35
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36 =item B<-intervals interval_file>
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37
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38 Specify the file containing the intervals to find the nearest features for,
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39 default settings require a BED compatible file
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40
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41 =item B<-features feature_file>
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42
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43 Specify the file containing the features that will be mapped against, default
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44 setting require a BED compatible file
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45
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46 =item B<-results ALL|CLOSEST>
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47
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48 The type of results to be reported. ALL will return all features within the
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49 specified window size from each interval in the file including any overlapping
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50 features. CLOSEST will return the closest feature within the window include
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51 overlapping features. The special case ENCOMPASSING FEATURE AND
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52 INTERNAL FEATURE override the closest distance. The first encountered
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53 ENCOMPASSING FEATURE will be returned in CLOSEST mode. If no ENCOMPASSING
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54 FEATURES exist, the first encountered INTERNAL FEATURE will be returned. If
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55 neither exists, the closest distance is used. The closest distance is determined
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56 by the shortest distance between either end of the interval and the feature
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57 (e.g. start-start, start-end, end-start, end-end).
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58
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59 The distance may also be ENCOMPASSING FEATURE or INTERNAL FEATURE. An
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60 encompassing feature is one which starts before an interval and ends
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61 after the interval. An internal feature is opposite where the feature
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62 is entirely within the interval.
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63
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64 DEFAULT:ALL
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65
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66 =item B<-direction BOTH|EITHER|UPSTREAM|DOWNSTREAM>
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67
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68 Direction is only used when CLOSEST is specified as the result type. BOTH
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69 will return both the closest upstream and downstream feature in the window.
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70 EITHER will return the closest regardless of whether it is upstream or
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71 downstream. DOWNSTREAM will return the closest feature with a midpoint to
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72 the right of midpoint of a + strand interval or the left of a - strand
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73 interval. UPSTREAM is just the opposite.
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74
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75 DEFAULT:BOTH
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76
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77 =item B<-window win_size>
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78
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79 Window size is the number of base pairs that will be considered upstream
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80 and downstream of an interval in which to find features. This also affects
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81 the performance of indexing and searching. Minimal testing suggests
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82 50000 bp to be roughly the optimal size, at least for Mus Musculus mm9/ncbim37.
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83
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84 MINIMUM:2500 DEFAULT:2500
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85
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86 =item B<-output output_file>
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87
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88 The file to report results to. The output format is a tab delimited file
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89 starting with the original line from the interval file followed by a list
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90 of matching features. Features are reported in the form of their name
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91 followed by the distance away in bp ascending from shortest distance to
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92 longest. e.g:
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93
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94 MY_INTERVAL_INFO ENS000001(20 bp distant) ENS000002 (350 bp distant) ...
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95
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96 The distance may also be ENCOMPASSING FEATURE or INTERNAL FEATURE. An
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97 encompassing feature is one which starts before an interval and ends
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98 after the interval. An internal feature is opposite where the feature
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99 is entirely within the interval.
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100
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101 DEFAULT:OFF
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102
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103 =item B<-include_capture>
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104
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105 Including capture information adds three columns to the output from
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106 feature_finder. These are the start and end location to capture all
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107 features found within the given window and the total distance in bp
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108 required to capture the entire set.
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109
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110 =item B<-promoter PROMOTOR_BP>
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111
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112 The start and end of the capture region will be modified to include
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113 the specified amount of the promoter region depending on the orientation
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114 of the feature. '+' strand features modify the start position while '-'
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115 strand features modify the end position.
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116
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117 DEFAULT:0
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118
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119 =item B<-icols interval_chrom_column:start:end:label:strand>
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120
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121 If the interval file is not in BED format, but still tab delimited -icols
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122 can be used to specify which columns in the file contain specific
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123 information. Column numbering begins with 1.
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124
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125 DEFAULT:1:2:3:4:6
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126
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127 =item B<-fcols feature_chrom_column:start:end:label:strand>
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128
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129 If the interval file is not in BED format, but still tab delimited -fcols
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130 can be used to specify which columns in the file contain specific
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131 information. Column numbering begins with 1.
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132
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133 DEFAULT:1:2:3:4:6
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134
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135 =item B<-html>
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136
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137 The output will be an HTML file with links to the features in the and
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138 the interval at the UCSC browser.
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139
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140 =item B<-db db_name>
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141
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142 Set the database for the organism to be used in the UCSC genome browser.
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143 Only used if an HTML output is specified.
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144
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145 DEFAULT:mm9
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146
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147 =item B<-cturl custom_track_url>
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148
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149 Define the URL to be used by the UCSC Genome Browser to load the custom
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150 tracks for display purposes. If left blank the URLs will show the windows
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151 defined by the input intervals, however the intervals themselves will not
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152 appear. Only used if an HTML output is specified.
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153
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154 =back
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155
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156 =head1 BUGS
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157
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158 =head1 REFERENCES
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159
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160 =head1 VERSION
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161
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162 0.1
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163
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164 =cut
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165
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166 #### END of POD documentation.
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167 #-----------------------------------------------------------------------------
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168
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169 use strict;
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170 use Getopt::Long;
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171 use Pod::Usage;
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172 use List::Util qw[min max];
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173
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174 my $path = $0;
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175 $path =~ s/\/\w*\.pl$//g;
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176 require "$path/feature_finder_methods.pl";
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177
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178 my $intervals;
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179 my $features;
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180 my $req_res_type = "All"; # "Closest"
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181 my $direction = "Both"; # "Upstream", "Downstream", "Both", "Either"
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182 my $out;
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183 my $window = 2500;
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184 my %feature_hash;
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185 my $help_flag;
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186 my $interval_cols = "1:2:3:4:6";
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187 my $feature_cols = "1:2:3:4:6";
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188 my $html;
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189 my $db = "mm9";
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190 my $cturl;
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191 my $debug = 0;
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192 my $include_capture = 0;
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193 my $promoter = 0;
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194
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195 my %options = (
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196 "direction|d=s" => \$direction,
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197 "intervals|i=s" => \$intervals,
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198 "features|f=s" => \$features,
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199 "results|r=s" => \$req_res_type,
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200 "output|o=s" => \$out,
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201 "window|w=s" => \$window,
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202 "icols=s" => \$interval_cols,
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203 "fcols=s" => \$feature_cols,
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204 "help|h" => \$help_flag,
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205 "html" => \$html,
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206 "db=s" => \$db,
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207 "cturl=s" => \$cturl,
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208 "include_capture|ic" => \$include_capture,
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209 "promoter|p=i" => \$promoter,
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210 "debug" => \$debug
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211 );
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212
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213 GetOptions(%options) or pod2usage(2);
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214 pod2usage(1) if $help_flag;
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215
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216 pod2usage({ message => "The window specified with -window must be at least 2500.\n", exitval => 2}) if ($window < 2500);
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217 #pod2usage({ message => "Result type specified with -result must be either $all or $close.\n", exitval => 2}) if (uc $req_res_type ne $all && uc $req_res_type ne $close);
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218 pod2usage({ message => "Direction sepecified with -direction must be one of BOTH, EITHER, UPSTREAM or DOWNSTREAM.\n", exitval => 2}) if (uc $direction ne "BOTH" && uc $direction ne "EITHER" && uc $direction ne "UPSTREAM" && uc $direction ne "DOWNSTREAM");
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219
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220 my @icols = split(":", $interval_cols);
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221 pod2usage({ message => "Must specify 5 columns with -icol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#icols != 4);
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222 my $ichrom = $icols[0]-1;
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223 my $istart = $icols[1]-1;
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224 my $iend = $icols[2]-1;
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225 my $ilabel = $icols[3]-1;
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226 my $istrand = $icols[4]-1;
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227
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228 my @fcols = split(":", $feature_cols);
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229 pod2usage({ message => "Must specify 5 columns with -fcol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#fcols != 4);
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230 my $fchrom = $fcols[0]-1;
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231 my $fstart = $fcols[1]-1;
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232 my $fend = $fcols[2]-1;
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233 my $flabel = $fcols[3]-1;
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234 my $fstrand = $fcols[4]-1;
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235
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236
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237 my $feature_hash_ref = &feature_index(\$features, \$window, \$fchrom, \$fstart, \$fend, \$debug);
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238 &process_intervals(\$intervals, \$out, $feature_hash_ref, \$req_res_type, \$direction, \$window, \$html, \$cturl, \$db, \$interval_cols, \$feature_cols, \$debug, \$display_distance, \$include_capture, \$promoter);
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239 exit(0);
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240
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241
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