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#!/usr/bin/perl
# Author: Katharina J. Hoff
# Date: February 19th 2018
# set stop codon frequencies in parameters.cfg of a particular species
use strict;
use Getopt::Long;
my $usage = "setStopCodonFreqs.pl --AUGUSTUS_CONFIG_PATH=path --species=someName --etrainOut=file\n";
my $AUGUSTUS_CONFIG_PATH;
my $species;
my $etrainOut;
my $help;
GetOptions( 'AUGUSTUS_CONFIG_PATH=s' => \$AUGUSTUS_CONFIG_PATH,
'species=s' => \$species,
'etrainOut=s' => \$etrainOut,
'help!' => \$help);
if($help){
print $usage;
exit 0;
}
if(not(defined($AUGUSTUS_CONFIG_PATH))){
if(-e $ENV{'AUGUSTUS_CONFIG_PATH'}){
$AUGUSTUS_CONFIG_PATH=$ENV{'AUGUSTUS_CONFIG_PATH'};
}else{
print $usage;
die("$AUGUSTUS_CONFIG_PATH missing!\n");
}
}
if(not(defined($species))){
print $usage;
die("No species defined!\n");
}
if(not(defined($etrainOut))){
print $usage;
die("No etraining output file defined!\n");
}
my $freqOfTag;
my $freqOfTaa;
my $freqOfTga;
open(ETRAIN, "<", $etrainOut) or die ("Could not open file $etrainOut!\n");
while(<ETRAIN>){
if(/tag:\s*.*\((.*)\)/){
$freqOfTag = $1;
}elsif(/taa:\s*.*\((.*)\)/){
$freqOfTaa = $1;
}elsif(/tga:\s*.*\((.*)\)/){
$freqOfTga = $1;
}
}
close(ETRAIN) or die ("Could not close file $etrainOut!\n");
my $cfgFile = "$AUGUSTUS_CONFIG_PATH/species/$species/$species\_parameters.cfg";
if(-e "$cfgFile"){
setParInConfig($cfgFile, "/Constant/amberprob", $freqOfTag);
setParInConfig($cfgFile, "/Constant/ochreprob", $freqOfTaa);
setParInConfig($cfgFile, "/Constant/opalprob", $freqOfTga);
}else{
die("Species config file $cfgFile does not seem to exist!\n");
}
sub setParInConfig{
my $configFileName = shift;
my $parName = shift;
my $value = shift;
open(CFGFILE, "+<$configFileName") or die ("Could not read config file $configFileName\n");
my @lines = <CFGFILE>;
foreach my $line (@lines){
$line =~ s/(\s*$parName +)(\S+?)(\s|\#|$)/$1$value$3/;
}
seek(CFGFILE, 0,0);
print CFGFILE @lines or die ("Could not write $configFileName");
truncate(CFGFILE, tell(CFGFILE));
close(CFGFILE);
}
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