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find_genomefeatures.pl
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find_genomefeatures.pl
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#!/usr/bin/perl -w
use strict;
use warnings;
use File::Path qw(make_path);
use File::Spec::Functions qw(catfile);
use Getopt::Std;
###########################################################################
# This script is designed to extract the following genomic features using #
# standard NCBI genome annotation files: GFF, PTT, RNT #
# #
# The following features will report in BED format: #
# mRNA, asmRNA, tRNA, rRNA, IGR #
# #
###########################################################################
my $fa;
my $fa_list;
my $gff;
my $ptt;
my $rnt;
my $out_path;
my $mRNA;
my $as;
my $igr;
my $rRNA;
my $tRNA;
my $mtrRNA;
my $gene;
my $chr_name;
parse_para();
find_features();
sub parse_para{
my %opts = ();
getopts("a:n:", \%opts);
usage() if(@ARGV != 1);
$out_path = $ARGV[0];
make_path($out_path) if( ! -d $out_path);
die("[-a] reference file required\n") if( ! defined $opts{a} );
my $fa_name = $fa = $opts{a};
$fa_name =~ s/\.f[n]*a//;
$gff = $fa_name . '.gff';
$ptt = $fa_name . '.ptt';
$rnt = $fa_name . '.rnt';
foreach my $f ("gff", "ptt", "rnt"){
my $ff = $fa_name . "." . $f;
die("[$f] file not found") if( ! -e $ff);
}
$mRNA = catfile($out_path, "mRNA.bed");
$as = catfile($out_path, "asmRNA.bed");
$igr = catfile($out_path, "IGR.bed");
$tRNA = catfile($out_path, "tRNA.bed");
$rRNA = catfile($out_path, "rRNA.bed");
$mtrRNA = catfile($out_path, "mtrRNA.bed");
$gene = catfile($out_path, "gene.bed");
### parse reference file
$fa_list = catfile($out_path, "ref.txt");
my $chr_length = 0;
($chr_name, $chr_length) = read_fa();
$chr_name = $opts{n} if defined $opts{n};
open my $fh_list, "> $fa_list" or die "Cannot write to fa_list file, $fa_list, $!\n";
print $fh_list $chr_name . "\t". $chr_length . "\n";
close $fh_list;
}
sub find_features{
open my $fh_mRNA, "> $mRNA" or die "$!";
open my $fh_as, "> $as" or die "$!";
open my $fh_igr, "> $igr" or die "$!";
open my $fh_tRNA, "> $tRNA" or die "$!";
open my $fh_rRNA, "> $rRNA" or die "$!";
# mRNA & AS
my %p = read_ptt();
foreach my $i (keys %p){
my ($chr, $length, $start, $end, $strand, $name) = split /\t/,$p{$i};
$start--; # bed file 0-left most
$end--;
print $fh_mRNA join("\t", ($chr_name, $start, $end, $name, $length, $strand)), "\n";
my $as_str = ($strand eq '+')?'-':'+';
print $fh_as join("\t", ($chr_name, $start, $end, "AS_".$name, $length, $as_str)), "\n";
}
close $fh_mRNA;
close $fh_as;
# rRNA & tRNA
my %t = read_rnt();
foreach my $m (keys %t){
if($m =~ /tRNA|Anticodon/){
print $fh_tRNA $t{$m}, "\n";
}elsif($m =~ /ribosomal\sRNA/){
print $fh_rRNA $t{$m}, "\n";
}else{
}
}
close $fh_tRNA;
close $fh_rRNA;
# IGR
extract_igr();
}
sub extract_igr {
my $igr_tmp = catfile($out_path, "igr_tmp.txt");
system("cat $mRNA $tRNA $rRNA | sort -k1,1 -k2,2n > $mtrRNA");
system("bedtools complement -i $mtrRNA -g $fa_list > $igr_tmp");
open my $fh_tmp, "< $igr_tmp" or die "Cannot open $igr_tmp, $!\n";
open my $fh_igr, "> $igr" or die "Cannot open $igr, $!\n";
my $counter = 0;
while(<$fh_tmp>) {
chomp;
my ($chr, $start, $end) = split /\t/, $_;
$start ++;
$end --;
my $igr_length = $end - $start + 1;
next if($igr_length < 20); ### skip the IGRs short than 20 bp
my $id_p = sprintf"IGR%04d", 2 * $counter;
my $id_n = sprintf"IGR%04d", 2 * $counter + 1;
print $fh_igr join("\t", $chr, $start, $end, $id_p, $igr_length, "+") . "\n";
print $fh_igr join("\t", $chr, $start, $end, $id_n, $igr_length, "-") . "\n";
$counter ++;
}
close $fh_tmp;
close $fh_igr;
unlink($igr_tmp) if( -e $igr_tmp );
unlink($mtrRNA) if( -e $mtrRNA );
}
sub read_fa{
my $chr_name;
my $chr_length;
my $header;
open my $fh_fa, "< $fa" or die "$!";
while(<$fh_fa>){
chomp;
if(/^\>/){
$_ =~ s/^\>//;
$header = $_;
}else{
$chr_length += length($_);
}
}
close $fh_fa;
$chr_name = (split /\s+/, $header)[0];
if($header =~ /\|/) {
$chr_name = (split /\|/, $header)[3];
}
return ($chr_name, $chr_length);
}
sub read_gff{
my %tabs = ();
my %ncRNA = ();
my $count = 0;
open my $fh_gff, "< $gff" or die "$!";
while(my $g = <$fh_gff>){
chomp ($g);
next if($g =~ /^\#/);
next unless($g =~ /\t(gene|ncRNA)/);
my ($chr, $start, $end, $strand, $des) = (split /\t/, $g)[0,3,4,6,8];
my $length = $end - $start + 1;
my $name = '-';
if(($name) = $des =~ /locus_tag=(\w+)/){
}elsif(($name) = $des =~ /Name=(\w+)/){
}elsif(($name) = $des =~ /ID=gene\:(\w+)/){
}elsif(($name) = $des =~ /GeneID\:(\d+)/){
}else{
}
my $id = join("\:", ($chr,$start, $end, $strand));
my $line = join "\t", ($chr, $length, $start, $end, $strand, $name);
if($g =~ /\tgene\t/){
$tabs{$id} = $line;
}elsif($g =~ /\tncRNA/){
$ncRNA{$id} = $line;
}
$count ++;
}
close $fh_gff;
die("not found gene in GFF file") if($count == 0);
foreach my $i (keys %ncRNA){
delete $tabs{$i};
}
return %tabs;
}
sub read_ptt{
my %out;
my $count = 0;
open my $fh_ptt, "< $ptt" or die "$!";
while(my $p = <$fh_ptt>){
chomp ($p);
next unless($p =~ /^\d+\.\.\d+/); # Skip the header line
my ($pos, $strand, $name) = (split /\t/, $p)[0,1,5];
my ($start, $end) = (split /\.+/, $pos)[0,1];
my $length = $end - $start + 1;
my $id = join("\:", ($chr_name, $start, $end, $strand));
$out{$id} = join "\t", ($chr_name, $length, $start, $end, $strand, $name);
$count ++;
}
close $fh_ptt;
die("found no lines in PTT file") if($count == 0);
return %out;
}
sub read_rnt{
my %out;
my $count = 0;
open my $fh_rnt, "< $rnt" or die "$!";
while(my $p = <$fh_rnt>){
chomp ($p);
next unless($p =~ /^\d+\.\.\d+/); # Skip the header line
my ($pos, $strand, $name, $type) = (split /\t/, $p)[0,1,5,8];
my ($start, $end) = (split /\.+/, $pos)[0,1];
my $length = $end - $start + 1;
$start --;
$end --;
my $line = join("\t", ($chr_name, $start, $end, $name, $length, $strand));
my $id = $name . ':' . $type;
$out{$id} = $line;
$count ++;
}
close $fh_rnt;
die("found no lines in PTT file") if($count == 0);
return %out;
}
sub usage {
die("
Usage: find_genomefeatures.pl [options] <outdir>
Options: -a : <STR> : fasta file of NCBI bacteria genome
need GFF, PTT, RNT files in the same dir
-n : <STR> : name of Chr for ouput
Note:
1. only output IGRs > 20 nt
Example:
find_genomefeatures.pl -a ~/NCBI/NC_000962.fna -n NC_000962.3 out
\n");
}