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#!/usr/bin/perl
# Authors: Katharina Hoff
# Contact: katharina.hoff@uni-greifswald.de
# This script converts the output of startAlign.pl to gtf format
use strict;
use warnings;
my $usage = "Usage\n\ngth2gtf.pl gth.gff3 gth.gtf\n\n";
if(scalar @ARGV != 2){
print $usage;
exit(1);
}
my $v = 4;
my $align = $ARGV[0];
my $out = $ARGV[1];
print STDOUT "\# " . (localtime) . ": Converting GenomeThreader file $align "
. "to gtf format\n" if ($v > 2);
open( GTH, "<", $align ) or die(
"ERROR in file " . __FILE__ ." at line ". __LINE__
. "\nCould not open file $align!\n");
open( GTHGTF, ">", $out ) or die(
"ERROR in file " . __FILE__ ." at line ". __LINE__
. "\nCould not open file $out!\n");
my $geneId;
# GTH may output alternative transcripts; we don't want to have any
# alternatives in training gene set, only print the first of any occuring
# alternatives
my %seen;
while (<GTH>) {
chomp;
my @gtfLine = split(/\t/);
if (m/\tgene\t/) {
my @idCol = split( /=/, $gtfLine[8] );
$geneId = $idCol[1];
}
elsif (m/\tCDS\t/) {
my @gtfLineLastCol = split( /;/, $gtfLine[8] );
my @gtfLineLastColField = split( /=/, $gtfLineLastCol[1] );
if (not( defined( $seen{ "$gtfLine[0]" . "_" . $geneId . "_" } ) )
)
{
$seen{ "$gtfLine[0]" . "_" . $geneId . "_" }
= "$gtfLine[0]" . "_"
. $geneId . "_"
. $gtfLineLastColField[1];
}
if ( $seen{ "$gtfLine[0]" . "_" . $geneId . "_" } eq "$gtfLine[0]"
. "_"
. $geneId . "_"
. $gtfLineLastColField[1] )
{
print GTHGTF "$gtfLine[0]\t$gtfLine[1]\t$gtfLine[2]\t"
. "$gtfLine[3]\t$gtfLine[4]\t$gtfLine[5]\t"
. "$gtfLine[6]\t$gtfLine[7]\tgene_id \""
. "$gtfLine[0]_g_" .$geneId . "_"
. $gtfLineLastColField[1] . "\"; transcript_id "
. "\"$gtfLine[0]_t" . "_" . $geneId . "_"
. $gtfLineLastColField[1] . "\";\n";
print GTHGTF "$gtfLine[0]\t$gtfLine[1]\texon\t$gtfLine[3]\t"
. "$gtfLine[4]\t$gtfLine[5]\t$gtfLine[6]\t"
. "$gtfLine[7]\tgene_id \"$gtfLine[0]_g" . "_"
. $geneId . "_"
. $gtfLineLastColField[1] . "\"; transcript_id \""
. "$gtfLine[0]_t" . "_" . $geneId . "_"
. $gtfLineLastColField[1] . "\";\n";
}
}
}
close(GTHGTF) or die("ERROR in file " . __FILE__ ." at line ". __LINE__
. "\nCould not close file $out!\n");
close(GTH) or die("ERROR in file " . __FILE__ ." at line ". __LINE__
. "\nCould not close file $align!\n");
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