map2.pl

map2.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] && $row->[2] eq 'gene') {
        my ($name_str)    = $row->[8] =~ /Name=([^;]+);/;
        my ($alias_str) = $row->[8] =~ /Alias=([^;]+);/;
        $name_str .= '0';
        $alias_str = join(",", map { $_.'0' } split ',', $alias_str);
        $row->[8] =~ s/Name=([^;]+);/Name=$name_str;/;
        $row->[8] =~ s/Alias=([^;]+);/Alias=$alias_str;/;  
    }
    elsif ($row->[2] && $row->[2] eq 'exon') {
        my ($parent_str)  = $row->[8] =~ /Parent=([^;]+);/;
        for my $parent_col (split ",", $parent_str) {
            $row->[8] =~ s/Parent=([^;]+);/Parent=$parent_col;/;
            print join("\t", @{ $row })."\n";
        }
        next;
    }
    print join("\t", @{ $row })."\n";
}