生物信息学习 之 Perl 脚本 -- 提取 lncRNA

脚本功能如说明所示：可以根据参考 gtf 文件 对 stringtie --merge 的结果文件进行过滤筛选新的 lncRNA。

#!/usr/bin/perl -w
use strict;

## this program can fetch that none reference gtf file from stringtie merged result 
## and filter that overlaped with know transcript in same strand 
## and filter that only have one exon

my $gtf = $ARGV[0];
my $stringtie_merged = $ARGV[1];

die "Usage:perl $0   \n" unless  @ARGV == 2;

my %reference;

open REF,$gtf or die "Can't open the reference gtf file $!";
while (){
    chomp;
    next if (/^$/);
    next if (/^#/);
    my @a = split /\t/,$_;
    my @b;

    if ($a[2] eq "transcript"){
        (my $id) = $_ =~ /\s+transcript_id\s+"(\S+)";/;
        push @b,$a[3];
        push @b,$a[4];
        $reference{$a[6]}{$a[0]}{$id} = \@b;
    }
}
close REF;

## deal with stringtie mered gtf file
my %transcript;
my %exon;
open IN,$stringtie_merged or die "Can't open the stringtie mweged gtf file $!";
while (){
    chomp;
    next if (/^$/);
    next if (/^#/);
    my @c = split /[\t;]/,$_;
    (my $id) = $_ =~ /\s+transcript_id\s+"(\S+)";/;
    if ($c[2] eq "transcript" && @c < 12) {
        my $strand = $c[6];
        my $start = $c[3];
        my $end = $c[4];
        my $chr = $c[0];
        my $z = $reference{$strand}{$chr};
        my $flag;
        foreach my $k (sort keys %$z) {
            if ($z->{$k}->[0] < $start && $z->{$k}->[1] > $start) {
                $flag++;
            }
            if ($z->{$k}->[0] > $start && $z->{$k}->[1] < $end) {
                $flag++;
            }
            if ($z->{$k}->[0] < $start && $z->{$k}->[1] > $end) {
                $flag++;
            }
            if ($z->{$k}->[0] < $end && $z->{$k}->[1] > $end) {
                 $flag++;
            }
        }
        if (not $flag) {
            $transcript{$id} = $_;
#            print "$_\n";
        }
    }
    if ($c[2] eq "exon" ) {
        push @{$exon{$id}},$_;
    }
}
close IN;

foreach my $k (sort keys %transcript) {
    if (@{$exon{$k}} > 1){
        print join ("\n",$transcript{$k},@{ $exon{$k} } )."\n";
    }

}
__END__