annotate nibls.pl @ 27:f2e18b4b1f3a draft

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author big-tiandm
date Thu, 06 Nov 2014 02:49:50 -0500
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1 #!/usr/bin/perl
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2 #####################################################################################################
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3 #LocusPocus is a free script, it is provided with the hope that you will enjoy, you may freely redistribute it at will. We would be greatful if you would keep these acknowledgements with it.
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4 #
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5 # Dan MacLean
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6 # dan.maclean@sainsbury-laboratory.ac.uk
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7 #
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8 # This program is free academic software; academic and non-profit
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9 # users may redistribute it freely.
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10 #
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11 # This program is distributed in the hope that it will be useful,
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12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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14 #
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15 # This software is released under GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
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16 # see included file GPL3.txt
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17 #
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18 #
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19
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20
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21 ###Dont forget you will need ...
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22 #####################################################################################################
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23 # Boost::Graph
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24 #Copyright 2005 by David Burdick
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25 # Available from http://search.cpan.org/~dburdick/Boost-Graph-1.2/Graph.pm
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26 #Boost::Graph is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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27 #####################################################################################################
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28
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29
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30
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31 use strict;
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32 use warnings;
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33 use Boost::Graph;
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34 use Getopt::Long;
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35
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36
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37 my $usage = "usage: $0 -f GFF_FILE [options]\n\n -m minimum inclusion distance (default 5)\n -c clustering coefficient (default 0.6) -b buffer between graphs (default 0) -k sample mark -o output file -t temp output file\n";
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38
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39 my $gff_file ;
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40 my $min_inc = 5;
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41 my $clus = 0.6;
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42 my $buff = 0;
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43 my $output_file;
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44 my $temp;
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45 my $mark;
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46
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47 GetOptions(
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48
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49 'c=f' => \$clus,
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50 'm=i' => \$min_inc,
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51 'f|file=s' => \$gff_file,
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52 'b=i' => \$buff,
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53 'o=s' => \$output_file,
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54 't=s' => \$temp,
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55 'k=s' => \$mark
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56 ) ;
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57
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58
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59 die $usage unless $gff_file;
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60
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61
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62 my $starttime = time;
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63 warn "started $starttime\n";
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64
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65 ## load in data
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66 my %molecules; # stores starts and ends of srnas
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67 open GFF, "<$gff_file";
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68
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69 while (my $entry = <GFF>){
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70
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71 chomp $entry;
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72 next if($entry=~/^\#/);
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73 my @data = split(/\t/,$entry);
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74 my $chr=shift @data;
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75 my $strand=shift @data;
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76 my $start=shift @data;
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77 my $end=shift @data;
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78 # my $length1=$end-$start+1;
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79 # if ($length1>30) {
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80 # $length1=40;
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81 # }
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82 my $total;
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83 for (my $s=0;$s<@data ;$s++) {
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84 $total+=$data[$s];
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85 }
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86 push @data,$total;
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87 # push @data,$length1;
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88 # if (defined $molecules{$chr}{$start}{$end}{$strand}) {
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89 # my @old_data=split(/;/,$molecules{$chr}{$start}{$end}{$strand});
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90 # for (my $i=0;$i<$#old_data ;$i++) {
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91 # $data[$i]+=$old_data[$i];
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92 # }
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93 # }
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94 my $data=join ";",@data;
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95 $molecules{$chr}{$start}{$end}{$strand} = $data;#chr#start#end#strand#add Tags information
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96 #print "$chr\t$start\t$end\n";
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97 }
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98
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99 close GFF;
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100
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101 warn "Data loaded...\nBuilding graphs and finding loci\nPlease be patient, this can take a while...\n";
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102
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103 my @sample=split/\#/,$mark;
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104 $mark=join"\"\t\"",@sample;
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105 open OUT, ">$output_file";
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106 print OUT "\"Chr\"\t\"MajorLength\"\t\"Percent\"\t\"$mark\"\n";
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107 open CLUSTER,">$temp";
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108 print CLUSTER "\#Chr\tMajorLength\tPercent\tTagsNumber\tTagsInfor\n";
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109 foreach my $chromosome (keys %molecules){
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110 my $g = new Boost::Graph(directed=>0);
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111 my @starts = keys(%{$molecules{$chromosome}} );
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112 @starts = sort {$a <=> $b} @starts;
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113
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114 while (my $srna_start = shift @starts){ ## work from left most sRNA to right most, add to graph if they close enough
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115
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116
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117 foreach my $srna_end (keys %{$molecules{$chromosome}{$srna_start}}){
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118
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119
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120 ###use new graph if the next srna is too far away from this one..
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121 if(defined $starts[0] and $srna_end + $min_inc + $buff < $starts[0]){
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122
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123
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124 ##dump the info from the old graph
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125 if (scalar(@{$g->get_nodes()}) > 2){
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126
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127 my $cluster_coeff = get_cc($g);
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128 if ($cluster_coeff >= $clus){
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129 dump_locus($g, $cluster_coeff);
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130 }
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131 }
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132
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133
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134 $g = new Boost::Graph(directed=>0);
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135
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136 }
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137
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138 foreach my $e (keys %{$molecules{$chromosome}{$srna_start}}){ ### extra bit because all loci with same start and different end overlap by definition. but are not collected by main search below
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139
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140 unless ($e eq $srna_end){
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141 my $sn = $chromosome. ':' . $srna_start . ':' . $srna_end; ## turn coordinate of sRNA inro a node name
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142 my $en = $chromosome. ':' . $srna_start . ':' . $e;
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143 $g->add_edge(node1=>"$sn", node2=>"$en", weight=>'1');
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144 }
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145
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146 }
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147
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148 foreach my $start (@starts){ ##build graph of overlaps
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149 my $new = 0;
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150 last if $start - $min_inc > $srna_end;
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151 if ($start - $min_inc <= $srna_end){
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152
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153 my $start_node = $chromosome . ':' . $srna_start . ':' . $srna_end;
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154 foreach my $end (keys %{$molecules{$chromosome}{$start}}){
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155
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156 my $end_node = $chromosome . ':' . $start . ':' . $end;
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157 $g->add_edge(node1=>"$start_node", node2=>"$end_node", weight=>'1');
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158 }
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159
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160 }
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161 }
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162 }
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163
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164 if (!(defined $starts[0])) {
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165 ##dump the info from the last graph
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166 if (scalar(@{$g->get_nodes()}) > 2){
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167
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168 my $cluster_coeff = get_cc($g);
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169 if ($cluster_coeff >= $clus){
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170 dump_locus($g, $cluster_coeff);
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171 }
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172 }
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173 }
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174 }
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175 }
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176
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177 warn "Loci printed\nFinished\n";
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178
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179 my $endtime = time;
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180
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181 my $elapsed = $endtime - $starttime;
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182
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183 warn "Time elapsed = $elapsed s\n";
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184 close OUT;
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185 close CLUSTER;
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186 #########################################################################################
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187 sub get_cc{ ## do cluster coeff calculation. No useful method anyway so self implemented NB, this is an undirected graph so k is n(n-1)/2
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188
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189 my $graph = shift;
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190
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191 my @component = @{$graph->get_nodes()}; #number of nodes
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192 my @clustering_coefficients;
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193
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194 foreach my $vertex (@component)
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195 {
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196
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197 my @neighbours = @{$graph->neighbors($vertex)};
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198
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199 my %edges_in_graph;
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200
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diff changeset
201 my $n = @neighbours; #n = the number of neighbours
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parents:
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202 my $k = ($n * ($n - 1))/2; #k = total number of possible connections
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parents:
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203
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parents:
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204 my $e= 0; #actual number of connections within sub-graph
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parents:
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205
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parents:
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206 foreach my $neighbour (@neighbours)
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parents:
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207 {
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parents:
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208 foreach my $neighbour_2 (@neighbours)
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parents:
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209 {
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parents:
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210 my $edge1 = "$neighbour\t$neighbour_2";
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big-tiandm
parents:
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211 my $edge2 = "$neighbour_2\t$neighbour";
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big-tiandm
parents:
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212 unless (exists $edges_in_graph{$edge1} or exists $edges_in_graph{$edge2})
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parents:
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213 {
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big-tiandm
parents:
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214 if ($graph->has_edge($neighbour, $neighbour_2) or $graph->has_edge($neighbour_2, $neighbour))
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big-tiandm
parents:
diff changeset
215 {
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parents:
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216 ++$e;
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parents:
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217 $edges_in_graph{$edge1}=1;
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big-tiandm
parents:
diff changeset
218 $edges_in_graph{$edge2}=1;
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parents:
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219 }
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parents:
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220 }
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big-tiandm
parents:
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221 }
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big-tiandm
parents:
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222 }
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big-tiandm
parents:
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223
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big-tiandm
parents:
diff changeset
224 if ($k >= 1)
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parents:
diff changeset
225 {
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parents:
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226 my $c = $e / $k;
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big-tiandm
parents:
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227 push @clustering_coefficients, $c;
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big-tiandm
parents:
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228 }
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parents:
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229 else {push @clustering_coefficients, '0';}
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parents:
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230 }
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parents:
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231
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parents:
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232 my $graph_n = scalar(@clustering_coefficients);
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parents:
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233 my $graph_cc = 0;
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parents:
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234 foreach my $cc (@clustering_coefficients){
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parents:
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235
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parents:
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236 $graph_cc = $graph_cc + $cc;
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parents:
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237
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parents:
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238 }
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parents:
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239 $graph_cc = $graph_cc / $graph_n;
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parents:
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240
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big-tiandm
parents:
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241 return $graph_cc;
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big-tiandm
parents:
diff changeset
242 }
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big-tiandm
parents:
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243
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big-tiandm
parents:
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244 ############################################################################################################
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big-tiandm
parents:
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245
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big-tiandm
parents:
diff changeset
246 sub dump_locus{
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big-tiandm
parents:
diff changeset
247
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big-tiandm
parents:
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248 my $g = shift;
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big-tiandm
parents:
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249 my $cc = shift;
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big-tiandm
parents:
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250 my $chr;
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big-tiandm
parents:
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251 my $start = 1000000000000000000000000000000000000000000000;
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big-tiandm
parents:
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252 my $end = -1;
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big-tiandm
parents:
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253 my @sample;
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big-tiandm
parents:
diff changeset
254 my @tag;
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big-tiandm
parents:
diff changeset
255 foreach my $node (@{$g->get_nodes()}){
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big-tiandm
parents:
diff changeset
256
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big-tiandm
parents:
diff changeset
257 $node =~ m/^(\S+):(\d+):(\d+)$/;
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big-tiandm
parents:
diff changeset
258 my $c=$1;
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big-tiandm
parents:
diff changeset
259 my $s=$2;
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big-tiandm
parents:
diff changeset
260 my $e=$3;
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big-tiandm
parents:
diff changeset
261 # my @data;
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big-tiandm
parents:
diff changeset
262 foreach my $str (keys %{$molecules{$c}{$s}{$e}}) {
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big-tiandm
parents:
diff changeset
263 my @data=split(/;/,$molecules{$c}{$s}{$e}{$str});
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big-tiandm
parents:
diff changeset
264 push @tag,($s.",".$e.",".$str.",".$data[-1]);
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big-tiandm
parents:
diff changeset
265 # for (my $i=0;$i<$#old_data ;$i++) {
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big-tiandm
parents:
diff changeset
266 # $data[$i]+=$old_data[$i];
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big-tiandm
parents:
diff changeset
267 # }
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big-tiandm
parents:
diff changeset
268 my $length=$e-$s+1;
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big-tiandm
parents:
diff changeset
269 if ($length>30) {
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big-tiandm
parents:
diff changeset
270 $length=40;
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big-tiandm
parents:
diff changeset
271 }
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big-tiandm
parents:
diff changeset
272 push @data,$length;
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big-tiandm
parents:
diff changeset
273 my $data=join ";",@data;#sample_exp/total_exp/length;
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big-tiandm
parents:
diff changeset
274 push @sample,$data;
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big-tiandm
parents:
diff changeset
275 }
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big-tiandm
parents:
diff changeset
276
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big-tiandm
parents:
diff changeset
277 $chr = $c;
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big-tiandm
parents:
diff changeset
278 $start = $s if $s < $start;
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big-tiandm
parents:
diff changeset
279 $end = $e if $e > $end;
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big-tiandm
parents:
diff changeset
280 }
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big-tiandm
parents:
diff changeset
281 my $tag=join";",@tag;
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big-tiandm
parents:
diff changeset
282 my $tag_number=@tag;
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big-tiandm
parents:
diff changeset
283 my ($max_length,$max_p,@cluster_exp)=Max_length(\@sample);
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big-tiandm
parents:
diff changeset
284 if ($max_length==40) {
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big-tiandm
parents:
diff changeset
285 $max_length="\>30";
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big-tiandm
parents:
diff changeset
286 }
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big-tiandm
parents:
diff changeset
287 my $cluster_exp=join"\t",@cluster_exp;
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big-tiandm
parents:
diff changeset
288 my $gff = $chr."\:$start\-$end\t".$max_length."nt\t".$max_p."\t" . $cluster_exp;
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big-tiandm
parents:
diff changeset
289 print CLUSTER "$chr\:$start\-$end\t$max_length"."nt\t$max_p\t$tag_number\t$tag\n";
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big-tiandm
parents:
diff changeset
290 print OUT $gff, "\n";
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big-tiandm
parents:
diff changeset
291 }
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big-tiandm
parents:
diff changeset
292
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big-tiandm
parents:
diff changeset
293 sub Max_length{
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big-tiandm
parents:
diff changeset
294 my @exp=@{$_[0]};
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big-tiandm
parents:
diff changeset
295 my %sample_length;
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big-tiandm
parents:
diff changeset
296 my $total_exp;
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big-tiandm
parents:
diff changeset
297 my @each;
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big-tiandm
parents:
diff changeset
298 for (my $i=0;$i<=$#exp ;$i++) {
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big-tiandm
parents:
diff changeset
299 my @tag=split/;/,$exp[$i];
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big-tiandm
parents:
diff changeset
300 my $length=pop(@tag);
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big-tiandm
parents:
diff changeset
301 my $exp=pop(@tag);
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big-tiandm
parents:
diff changeset
302 $sample_length{$length}+=$exp;
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big-tiandm
parents:
diff changeset
303 $total_exp+=$exp;
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big-tiandm
parents:
diff changeset
304 for (my $j=0;$j<=$#tag ;$j++) {
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big-tiandm
parents:
diff changeset
305 $each[$j]+=$tag[$j];
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big-tiandm
parents:
diff changeset
306 }
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big-tiandm
parents:
diff changeset
307 }
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big-tiandm
parents:
diff changeset
308 my $max=0;
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big-tiandm
parents:
diff changeset
309 my $max_key;
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big-tiandm
parents:
diff changeset
310 foreach my $key (sort keys %sample_length) {
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big-tiandm
parents:
diff changeset
311 my $p=$sample_length{$key}/$total_exp;
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big-tiandm
parents:
diff changeset
312 if ($p>$max) {
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big-tiandm
parents:
diff changeset
313 $max=$p;
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big-tiandm
parents:
diff changeset
314 $max_key=$key;
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big-tiandm
parents:
diff changeset
315 }
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big-tiandm
parents:
diff changeset
316 $sample_length{$key}=sprintf("%.2f",$p);
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big-tiandm
parents:
diff changeset
317 }
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big-tiandm
parents:
diff changeset
318 return($max_key,$sample_length{$max_key},@each);
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big-tiandm
parents:
diff changeset
319 }