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#!/usr/bin/perl -w
# Program to parse bzip2'ed output from a set of warg runs done gene-by-gene
# Run from within the directory containing the .bz2 files
# Generates text summary files that can be plotted using genomeplots_log.R
# Usage: rhomulus.pl <warg output base filename> <# of genes> <file with mapping from warg run ID to gene ID> <path to alignment files> <file containing gene coordinates in the reference genome>
#
# @author Aaron Darling
# @license GPL
use strict;
my $basename = $ARGV[0];
my $maxgenes = $ARGV[1];
my $decoder = $ARGV[2];
my $genpath = $ARGV[3];
my $coords = $ARGV[4];
die unless @ARGV==5;
my @stats=("rho","theta","delta","tmrca");
# read in gene ID decoder
my %geneId;
open( DECOD, "$decoder" ) || die "unable to open decoder $decoder\n";
while( my $line = <DECOD> )
{
chop($line);
my @stuff = split( /:/, $line );
$geneId{$stuff[0]} = $stuff[1];
}
open(RHO, ">rho_summary.txt");
open(THETA, ">theta_summary.txt");
open(TMRCA, ">tmrca_summary.txt");
open(DELTA, ">delta_summary.txt");
open(RHOTHETA, ">rhotheta_summary.txt");
open(RHOPERSITE, ">rhopersite_summary.txt");
open(RHODELTA, ">rhodelta_summary.txt");
open(ROVERM, ">roverm_summary.txt");
# read in gene position table
my %lends;
my %rends;
my %strands;
open( COORD, "$coords") || die "Unable to open $coords\n";
while( my $line = <COORD> )
{
my @stuff = split( /\s+/, $line );
$lends{$stuff[4]} = $stuff[0];
$rends{$stuff[4]} = $stuff[1];
$strands{$stuff[4]} = $stuff[2];
}
for( my $gI = 1; $gI < $maxgenes; $gI++ )
{
my $bzfname = "$basename.$gI.xml.bz2";
print STDERR "Trying $bzfname\n";
next unless -e $bzfname;
# look up position in the genome
my $alnfile = $genpath."/".$geneId{$gI};
open( ALN, $alnfile ) || die "Error opening $alnfile\n";
my $geneid = 0;
while( my $line = <ALN> )
{
next unless $line =~ /(ESCO001c01_\d+)/;
$geneid = $1;
last;
}
# read posterior file
open( POST, "bzcat $bzfname |" ) || next;
my @rho;
my @theta;
my @tmrca;
my @delta;
my @redgelens;
my @curredges;
my $prevredge = 0; # whether the previous line had a recedge
while( my $line = <POST> )
{
checkLine($line,"rho",\@rho);
checkLine($line,"theta",\@theta);
checkLine($line,"tmrca",\@tmrca);
checkLine($line,"delta",\@delta);
my $tmp = checkRecEdge($line,\@curredges);
if($tmp == 0 && $prevredge == 1)
{
push( @redgelens, [ @curredges ] );
@curredges = ();
}
$prevredge = $tmp;
}
# file is parsed, summarize stats
print RHO summaryLine($geneid,\@rho);
print THETA summaryLine($geneid,\@theta);
print TMRCA summaryLine($geneid,\@tmrca);
print DELTA summaryLine($geneid,\@delta);
# compute rho over thetas
my @rhotheta = @rho;
for(my $j = 0; $j<@rhotheta;$j++){ $rhotheta[$j]/=$theta[$j];}
print RHOTHETA summaryLine($geneid,\@rhotheta);
my @rhopersite = @rho;
my $L = $rends{$geneid}-$lends{$geneid};
for(my $j = 0; $j<@rhopersite;$j++){ $rhopersite[$j]/=($delta[$j]+$L-1);}
print RHOPERSITE summaryLine($geneid,\@rhopersite);
my @rhodelta = @rhopersite;
for(my $j = 0; $j<@rhopersite;$j++){ $rhodelta[$j]*=$delta[$j];}
print RHODELTA summaryLine($geneid,\@rhodelta);
# calculate Xavier's Y for r/m
my @roverm = @rhodelta;
for(my $j=0; $j<@redgelens; $j++){
my $Y = 0;
my $cur = $redgelens[$j];
for( my $k=0; $k<@$cur; $k++)
{
$Y += 0.75*(1.0-exp(-(4.0/3.0)*$theta[$j]*@$cur[$k]/$L));
}
$Y /= @$cur;
$roverm[$j] *= $Y;
}
print ROVERM summaryLine($geneid,\@roverm);
}
sub checkLine {
my $linea = shift;
my $stat = shift;
my $statts = shift;
if( $linea =~ /$stat\>(\d+)\.(\d+)\<\/$stat/ )
{
my $rv = $2;
$rv /= 10 while( $rv > 1 );
$rv += $1;
push( @$statts, $rv );
}elsif( $linea =~ /$stat\>(\d+)\<\/$stat/ )
{
push( @$statts, $1 );
}
}
sub summaryLine {
my $gid = shift;
my $tmp = shift;
my @stats = @$tmp;
my $sum = 0;
foreach( @stats ){
$sum += $_;
}
my $mean = $sum/@stats;
my @sorted = sort { $a <=> $b } @stats;
my $sd = 0;
foreach( @stats ){
$sd += ($mean-$_)*($mean-$_);
}
$sd /= @stats;
$sd = sqrt($sd);
my $l = $lends{$gid};
my $r = $rends{$gid};
my $s = $strands{$gid};
my $liner = "$gid\t$mean\t$sd\t$l\t$r\t$s\t";
$liner .= $sorted[0]."\t".$sorted[@sorted*0.1]."\t".$sorted[@sorted*0.25]."\t".$sorted[@sorted*.5]."\t".$sorted[@sorted*.75]."\t".$sorted[@sorted*.9]."\t".$sorted[@sorted-1]."\n";
return $liner;
}
sub checkRecEdge {
my $linea = shift;
my $redgelens = shift;
return 0 unless( $linea =~ /\<recedge\>/);
if( $linea =~ /\<afrom\>(.+)\<\/afrom\>\<ato\>(.+)\<\/ato\>/ )
{
push( @$redgelens, abs($1-$2) );
}
return 1;
}
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