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|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 annot.gff3 target_file.txt\n\n";
my $annot_gff3 = $ARGV[0] or die $usage;
my $target_file = $ARGV[1] or die $usage;
main: {
my %trans_id_to_annot = &parse_trans_names($annot_gff3);
open (my $fh, $target_file) or die "Error, cannot open file $target_file";
while (<$fh>) {
chomp;
my @x = split(/\t/);
if (my $name = $trans_id_to_annot{ $x[0] }) {
$x[0] .= " $name";
$x[0] =~ s/\s/_/g;
}
print join("\t", @x) . "\n";
}
close $fh;
exit(0);
}
####
sub parse_trans_names {
my ($gff3_file) = @_;
my %gene_to_name;
my %mRNA_to_gene;
open (my $fh, $gff3_file) or die "Error, cannot open file $gff3_file";
while (<$fh>) {
unless (/\w/) { next; }
my @x = split(/\t/);
my $feat_type = $x[2];
my $info = $x[8];
if ($info =~ /ID=([^;]+)/) {
my $id = $1;
if ($feat_type eq "mRNA") {
$info =~ /Parent=([^;]+)/ or die "Error, cannot get parent info from $_";
my $gene = $1;
$mRNA_to_gene{$id} = $gene;
}
elsif ($feat_type eq "gene") {
$info =~ /Name=(.*)/ or die "Error, cannot get name from $_";
my $name = $1;
$gene_to_name{$id} = $name;
}
}
}
close $fh;
my %trans_to_name;
foreach my $mRNA (keys %mRNA_to_gene) {
my $gene = $mRNA_to_gene{$mRNA};
my $name = $gene_to_name{$gene};
$trans_to_name{$mRNA} = $name;
}
return(%trans_to_name);
}
|
