A Genbank to BED converter

Like the previous Genbank -> GTF converter, this script is also depended on BioPerl, so you need firstly get the module installed in your system (Install BioPerl). To check whether BioPerl is ready, just refer to this post: bio-spring.info/check-bioperl/ .

SYNOPSIS


gb2bed.pl [options] filename

Options:
--help -h display this message
--input -i NCBI GenBank file
--out -o filename of bed output. [STDOUT]
--filter -f GenBank primary tag that will be filtered, may be set to 'gene', 'CDS', 'rRNA', etc.
--keep -k GenBank primary tag will be keep. Default is CDS. [CDS]

Examples:

perl gb2bed.pl -i seq.gb -o seq.bed
perl gb2bed.pl -i seq.gb -k CDS -o seq.bed
perl gb2bed.pl seq.gb > seq.bed

Read Pod for further information.


#!/usr/bin/perl

=pod

=head1 NAME

gb2bed.pl -- Genbank -> BED

=head1 SYNOPSIS

gb2bed.pl [options] filename

Options:
--help -h display this message
--input -i NCBI GenBank file
--out -o filename of bed output. [STDOUT]
--filter -f GenBank primary tag that will be filtered, may be set to 'gene', 'CDS', 'rRNA', etc.
--keep -k GenBank primary tag will be keep. Default is CDS. [CDS]

Examples:

perl gb2bed.pl -i seq.gb -o seq.bed
perl gb2bed.pl -i seq.gb -k CDS -o seq.bed
perl gb2bed.pl seq.gb > seq.bed

=head1 DESCRIPTION

Use this program to generate bioconductor friendly BED files from NCBI GenBank.
Six columns will be extracted:
1. chrom - name of the chromosome or scaffold. Any valid seq_region_name can be used, and chromosome names can be given with or without the 'chr' prefix.
2. chromStart - Start position of the feature in standard chromosomal coordinates (i.e. first base is 0).
3. chromEnd - End position of the feature in standard chromosomal coordinates
4. name - Label to be displayed under the feature, if turned on in "Configure this page". [locus_tag]
5. score - A score between 0 and 1000. [0]
6. strand - defined as + (forward) or - (reverse).

=head1 AUTHOR

Chun-Hui, Gao (gaoch@thelifesciencecentury.com)
Copyright (c) 2015 www.thelifesciencecentury.com.

=cut

use strict;
use Data::Dumper;
use Pod::Usage;
use Bio::SeqIO;
use Getopt::Long;

my ($help, $genbank_input, $output, @filters, @keep);

my $ok= GetOptions( 'help|h' => \$help,
'input|i=s' => \$genbank_input,
'filter|f=s' => \@filters,
'keep|k=s' => \@keep,
'out|o=s' => \$output );
pod2usage(2) if $help || !$ok;

$genbank_input = shift @ARGV unless ($genbank_input );

@keep = ('gene') unless $#keep >= 0;

open *IN, "< $genbank_input " or die pod2usage(2); my $out; if ($output) { open $out, "> $output" or die "Can't open file $output:$@\n";
}
else {
$out = *STDOUT;
}

my %filter;
map {$filter{$_}++} @filters;
my %keep;
map {$keep{$_}++} @keep;
my $in = Bio::SeqIO->new(-fh => \*IN, -format => "genbank");
while ( my $seq = $in->next_seq() ) {
my $chr = $seq->accession_number;

my @all_SeqFeatures = $seq->get_all_SeqFeatures;

#~ warn "# working on $chr\n";
if ($#filters >= 0){
@all_SeqFeatures = grep { !defined $filter{$_->primary_tag} } @all_SeqFeatures;
}
if ($#keep >= 0) {
@all_SeqFeatures = grep { defined $keep{$_->primary_tag} } @all_SeqFeatures;
}

# abort if there are no features
warn "$chr has no features, skipping\n" and next
if $#all_SeqFeatures < 0; for my $feature ( @all_SeqFeatures ) { my ($start, $end, $name, $strand); $start = $feature->start - 1; # bed base is 0, while genbank is 1
$end = $feature->end;
($name) = $feature->get_tag_values('locus_tag');
$strand = $feature->strand;
$strand = $strand < 0 ? '-' : '+'; print $out join("\t", $chr, $start, $end, $name, 0, $strand), "\n"; } }

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