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parse_region_from_genome.pl
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#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
my $gbk = $ARGV[0];
my $up = $ARGV[1];
my $down = $ARGV[2];
my $region = $ARGV[3];
unless(defined $ARGV[0] and $ARGV[1] and $ARGV[2] and $ARGV[3]) { die("usage: ./parse_region_from_genome.pl NC_DDDDDD ntup(number) ntdown(number) region(i.e. 5utr/3utr/cds) > outfile.fas\n"); }
# comment: with up 200 donw 100 the startcodon is on position 201 202 203 of the 300 nt long string
my $in = Bio::SeqIO->new(-file => $gbk , '-format' => 'genbank');
my $seq = $in->next_seq();
my $in2 = Bio::SeqIO->new(-file => $gbk , '-format' => 'genbank');
if ($region eq "5utr") {
while ( my $seq2 = $in2->next_seq() ) {
foreach my $sf2 ( $seq2->get_SeqFeatures() ) {
if( $sf2->primary_tag eq 'CDS' ) {
my $ltag = "";
if ($sf2->has_tag("locus_tag")) {
my @ltaglist = $sf2->get_tag_values("locus_tag");
$ltag = $ltaglist[0];
}
my $start = $sf2->start;
my $end = $sf2->end;
my $loc = $sf2->location->strand;
if($loc == 1) {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = ();
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->start);
}
print &get_region(1, $locarray[0], $up, $down, $ltag, $seq);
} else {
print &get_region(1, $start, $up, $down, $ltag, $seq);
}
} else {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = ();
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->end);
}
print &get_region(-1, $locarray[-1], $up, $down, $ltag, $seq);
} else {
print &get_region(-1, $end, $up, $down, $ltag, $seq);
}
}
}
}
}
}
if ($region eq "3utr") {
while ( my $seq2 = $in2->next_seq() ) {
foreach my $sf2 ( $seq2->get_SeqFeatures() ) {
if( $sf2->primary_tag eq 'CDS' ) {
my $ltag = "";
if ($sf2->has_tag("locus_tag")) {
my @ltaglist = $sf2->get_tag_values("locus_tag");
$ltag = $ltaglist[0];
}
my $start = $sf2->start;
my $end = $sf2->end;
my $loc = $sf2->location->strand;
if($loc == 1) {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = ();
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->end);
}
print &get_region(1, ($locarray[-1] + 1), $up, $down, $ltag, $seq);
} else {
print &get_region(1, ($end + 1), $up, $down, $ltag, $seq);
}
} else {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = ();
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->start);
}
print &get_region(-1, ($locarray[0] - 1), $up, $down, $ltag, $seq);
} else {
print &get_region(-1, ($start - 1), $up, $down, $ltag, $seq);
}
}
}
}
}
}
if ($region eq "cds") {
while ( my $seq2 = $in2->next_seq() ) {
foreach my $sf2 ( $seq2->get_SeqFeatures() ) {
if( $sf2->primary_tag eq 'CDS' ) {
my $ltag = "";
if ($sf2->has_tag("locus_tag")) {
my @ltaglist = $sf2->get_tag_values("locus_tag");
$ltag = $ltaglist[0];
}
my $start = $sf2->start;
my $end = $sf2->end;
my $loc = $sf2->location->strand;
my $tempStart = $start;
my $tempUp = $up;
my $tempDown = $down;
if($loc == 1) {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = (); # ends
my @locarray2 = (); # starts
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->end);
push(@locarray2,$location->start);
}
my $printseq1 = &get_region_cds(1, $locarray2[0], $up, 0, $ltag, $seq);
chomp $printseq1;
my $printseq2 = $sf2->spliced_seq->seq;
my $printseq3 = &get_region_cds(1, ($locarray[-1] + 1), 0, $down, $ltag, $seq);
$printseq3 =~ s/>.*\n//; # remove locus_tag
my $printseq = $printseq1 . $printseq2 . $printseq3;
print $printseq;
} else {
if ($tempStart==1) {
$start++;
$tempUp++;
}
my $printseq1 = &get_region_cds(1, $start, $tempUp, 0, $ltag, $seq);
chomp $printseq1;
chop $printseq1 if($tempStart == 1);
my $printseq2 = $sf2->spliced_seq->seq;
my $printseq3 = &get_region_cds(1, $end, 0, ($down + 1), $ltag, $seq);
$printseq3 =~ s/>.*\n//; # remove locus_tag
$printseq3 = reverse($printseq3);
chop $printseq3;
$printseq3 = reverse($printseq3);
my $printseq = $printseq1 . $printseq2 . $printseq3;
print $printseq;
}
} else {
if ( $sf2->location->isa('Bio::Location::SplitLocationI') ) {
my @locarray = (); # starts
my @locarray2 = (); # ends
foreach my $location ( $sf2->location->sub_Location ) {
push(@locarray,$location->start);
push(@locarray2,$location->end);
}
my $printseq1 = &get_region_cds(-1, $locarray2[-1], $up, 0, $ltag, $seq);
chomp $printseq1;
my $printseq2 = $sf2->spliced_seq->seq;
my $printseq3 = &get_region_cds(-1, ($locarray[0] - 1), 0, $down, $ltag, $seq);
$printseq3 =~ s/>.*\n//; # remove locus_tag
my $printseq = $printseq1 . $printseq2 . $printseq3;
print $printseq;
} else {
if ($tempStart==1) {
$start++;
$tempDown++;
}
my $printseq1 = &get_region_cds(-1, ($end - 1), ($up + 1), 0, $ltag, $seq);
chomp $printseq1;
chop $printseq1;
my $printseq2 = $sf2->spliced_seq->seq;
my $printseq3 = &get_region_cds(-1, ($start - 1), 0, $tempDown, $ltag, $seq);
$printseq3 =~ s/>.*\n//; # remove locus_tag
if ($tempStart==1) {
$printseq3 = reverse($printseq3);
chop $printseq3;
$printseq3 = reverse($printseq3);
}
my $printseq = $printseq1 . $printseq2 . $printseq3;
print $printseq;
}
}
}
}
}
}
# subs
sub get_region
{
my $strand = $_[0];
my $pos = $_[1];
my $upstream = $_[2];
my $downstream = $_[3];
my $ltag = $_[4];
my $seq_obj = $_[5];
my $genomelength = $seq_obj->length;
my $circularTest = $seq_obj->is_circular;
if ($strand == -1) {
if ((($pos - $downstream) >= 1) and (($pos + $upstream) <= $genomelength)) {
my $printseq = reverse($seq_obj->subseq(($pos - $downstream + 1), ($pos + $upstream)));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
} else { # this exception deals with sequences at the sides of the genome
unless($circularTest) { # only do this if genome is not curcular
if (($pos - $downstream) < 1) {
my $printseq = reverse($seq_obj->subseq(1, ($pos + $upstream)));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
if (length($printseq) >= 140) {
return ">$ltag\n$printseq\n";
} else { return; }
}
if (($pos + $upstream) > $genomelength) {
my $printseq = reverse($seq_obj->subseq(($pos - $downstream + 1), $genomelength));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
if (length($printseq) >= 140) {
return ">$ltag\n$printseq\n";
} else { return; }
}
} else { # here we add the exception for the edges in circular genomes
if (($pos - $downstream) < 1) {
my $overhang = ($pos - $downstream) * (-1);
my $printseq1 = reverse($seq_obj->subseq(1, ($pos + $upstream)));
my $printseq2 = reverse($seq_obj->subseq(($genomelength - $overhang + 1), $genomelength));
my $printseq = $printseq1 . $printseq2;
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
if (($pos + $upstream) > $genomelength) {
my $overhang = ($pos + $upstream) - $genomelength;
my $printseq1 = reverse($seq_obj->subseq(1, $overhang));
my $printseq2 = reverse($seq_obj->subseq(($pos - $downstream + 1), $genomelength));
my $printseq = $printseq1 . $printseq2;
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
}
}
} else {
if ((($pos - $upstream) >= 1) and (($pos + $downstream) <= $genomelength)) {
my $printseq = $seq_obj->subseq(($pos - $upstream), ($pos + $downstream - 1));
return ">$ltag\n$printseq\n";
} else { # this exception deals with sequences at the sides of the genome
unless($circularTest) { # only do this if genome is not curcular
if (($pos - $upstream) < 1) {
my $printseq = $seq_obj->subseq(1, ($pos + $downstream - 1));
if (length($printseq) >= 140) {
return ">$ltag\n$printseq\n";
} else { return; }
}
if (($pos + $downstream) > $genomelength) {
my $printseq = $seq_obj->subseq(($pos - $upstream), $genomelength);
if (length($printseq) >= 140) {
return ">$ltag\n$printseq\n";
} else { return; }
}
} else { # here we add the exception for the edges in circular genomes
if (($pos - $upstream) < 1) {
my $overhang = ($pos - $upstream) * (-1);
my $printseq2 = $seq_obj->subseq(1, ($pos + $downstream - 1));
my $printseq1 = $seq_obj->subseq(($genomelength - $overhang), $genomelength);
my $printseq = $printseq1 . $printseq2;
return ">$ltag\n$printseq\n";
}
if (($pos + $downstream) > $genomelength) {
my $overhang = ($pos + $downstream) - $genomelength;
my $printseq1 = $seq_obj->subseq(($pos - $upstream), $genomelength);
my $printseq2 = $seq_obj->subseq(1, ($overhang - 1));
my $printseq = $printseq1 . $printseq2;
return ">$ltag\n$printseq\n";
}
}
}
}
}
sub get_region_cds
{
my $strand = $_[0];
my $pos = $_[1];
my $upstream = $_[2];
my $downstream = $_[3];
my $ltag = $_[4];
my $seq_obj = $_[5];
my $genomelength = $seq_obj->length;
my $circularTest = $seq_obj->is_circular;
if ($strand == -1) {
if ((($pos - $downstream) >= 1) and (($pos + $upstream) <= $genomelength)) {
my $printseq = reverse($seq_obj->subseq(($pos - $downstream + 1), ($pos + $upstream)));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
} else { # this exception deals with sequences at the sides of the genome
unless($circularTest) { # only do this if genome is not curcular
if (($pos - $downstream) < 1) {
my $printseq = reverse($seq_obj->subseq(1, ($pos + $upstream)));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
if (($pos + $upstream) > $genomelength) {
my $printseq = reverse($seq_obj->subseq(($pos - $downstream + 1), $genomelength));
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
} else { # here we add the exception for the edges in circular genomes
if (($pos - $downstream) < 1) {
my $overhang = ($pos - $downstream) * (-1);
my $printseq1 = reverse($seq_obj->subseq(1, ($pos + $upstream)));
my $printseq2 = reverse($seq_obj->subseq(($genomelength - $overhang + 1), $genomelength));
my $printseq = $printseq1 . $printseq2;
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
if (($pos + $upstream) > $genomelength) {
my $overhang = ($pos + $upstream) - $genomelength;
my $printseq1 = reverse($seq_obj->subseq(1, $overhang));
my $printseq2 = reverse($seq_obj->subseq(($pos - $downstream + 1), $genomelength));
my $printseq = $printseq1 . $printseq2;
$printseq =~ tr/[g,a,t,c,G,A,T,C]/[c,t,a,g,C,T,A,G]/;
return ">$ltag\n$printseq\n";
}
}
}
} else {
if ((($pos - $upstream) >= 1) and (($pos + $downstream) <= $genomelength)) {
my $printseq = $seq_obj->subseq(($pos - $upstream), ($pos + $downstream - 1));
return ">$ltag\n$printseq\n";
} else { # this exception deals with sequences at the sides of the genome
unless($circularTest) { # only do this if genome is not curcular
if (($pos - $upstream) < 1) {
my $printseq = $seq_obj->subseq(1, ($pos + $downstream - 1));
return ">$ltag\n$printseq\n";
}
if (($pos + $downstream) > $genomelength) {
my $printseq = $seq_obj->subseq(($pos - $upstream), $genomelength);
return ">$ltag\n$printseq\n";
}
} else { # here we add the exception for the edges in circular genomes
if (($pos - $upstream) < 1) {
my $overhang = ($pos - $upstream) * (-1);
my $printseq2 = $seq_obj->subseq(1, ($pos + $downstream - 1));
my $printseq1 = $seq_obj->subseq(($genomelength - $overhang), $genomelength);
my $printseq = $printseq1 . $printseq2;
return ">$ltag\n$printseq\n";
}
if (($pos + $downstream) > $genomelength) {
my $overhang = ($pos + $downstream) - $genomelength;
my $printseq1 = $seq_obj->subseq(($pos - $upstream), $genomelength);
my $printseq2 = $seq_obj->subseq(1, ($overhang - 1));
my $printseq = $printseq1 . $printseq2;
return ">$ltag\n$printseq\n";
}
}
}
}
}