map1.pl

map1.pl

use strict;
use warnings;
use Text::CSV_XS;
use Data::Printer;

my $csv = Text::CSV_XS->new({ binary => 1, sep_char => "\t" });
open my $fh, "<", $ARGV[0] or die $!;
open my $fh2, "<", $ARGV[1] or die $!;

# 1. 키맵 생성
my %map = ();
while(my $row = $csv->getline($fh)) {
    $map{$row->[0]} = $row->[1];
}

my $count = 0;
while(my $row = $csv->getline($fh2)) {
    if ($row->[2] && $row->[2] eq 'exon') {
        my $description = $row->[8];
        my ($val) = $description =~ /Parent=([^;]+);/;
        my $str = join(",", map { my $r = $_; $r =~ s/^0:+//g; $map{$r} ? $map{$r} : $r;  } split ",", $val);
        $row->[8] =~ s/Parent=[^;]+;/Parent=$str;/;
    }
    elsif ($row->[2] && $row->[2] =~ /^(?:gene|mRNA)$/) {
        my $description = $row->[8];
        my ($val) = $description =~ /Alias=([^;]+);/;
        my $str = join(",", map { my $r = $_; $r =~ s/^0:+//g; $map{$r} ? $map{$r} : $r;  } split ",", $val);
        $row->[8] =~ s/Alias=[^;]+;/Alias=$str;/;
    }
    print join("\t", @{ $row })."\n";
}

$ perl map.pl genome_mapping_update.txt iceplant_gene.gff > result1.txt