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#FILE: sequence_to_multi_fasta.pl
#AUTH: Paul Stothard <stothard@ualberta.ca>
#DATE: June 22, 2020
#VERS: 1.2
use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;
use Bio::SeqUtils;
my %options = (
input => undef,
output => undef,
size => undef,
overlap => undef,
title => undef,
type => undef,
help => undef
);
Getopt::Long::Configure('bundling');
GetOptions(
'i=s' => \$options{'input'},
'o=s' => \$options{'output'},
's=i' => \$options{'size'},
'v=i' => \$options{'overlap'},
'h|help' => \$options{'help'}
);
if ( defined( $options{'help'} ) ) {
_usage();
exit(0);
}
if ( !( defined( $options{'input'} ) ) ) {
_usage();
exit(1);
}
if ( !( defined( $options{'output'} ) ) ) {
_usage();
exit(1);
}
my $seqObject = _getSeqObject( \%options );
if ( ( $options{"type"} eq "embl" ) || ( $options{"type"} eq "genbank" ) ) {
$options{"accession"} = $seqObject->accession_number;
if ( !( defined( $options{"title"} ) ) ) {
$options{"title"} = $seqObject->description();
}
}
if ( $options{"type"} eq "fasta" ) {
if ( !( defined( $options{"title"} ) ) ) {
$options{"title"} = $seqObject->description();
}
}
if ( !( defined( $options{"title"} ) ) ) {
$options{"title"} = "split";
}
my $dna = $seqObject->seq();
my $length = length($dna);
$options{'title'} =~ s/\s+/_/g;
if ( !( defined( $options{'size'} ) ) ) {
$options{'size'} = $length;
}
open( OUTFILE, ">" . $options{"output"} ) or die("Cannot open file : $!");
for ( my $i = 0 ; $i < $length ; $i = $i + $options{'size'} ) {
#if using overlap adjust $i
if ( ( defined( $options{'overlap'} ) ) && ( $i > $options{'overlap'} ) ) {
$i = $i - $options{'overlap'};
}
my $start = $i + 1;
my $subseq = substr( $dna, $i, $options{'size'} );
my $subseq_length = length($subseq);
my $end = $start + $subseq_length - 1;
print( OUTFILE ">"
. $options{'title'}
. "_start=$start;end=$end;length=$subseq_length;source_length=$length\n$subseq\n"
);
}
close(OUTFILE) or die("Cannot close file : $!");
sub _getSeqObject {
my $options = shift;
open( INFILE, $options->{'input'} ) or die("Cannot open input file: $!");
while ( my $line = <INFILE> ) {
if ( !( $line =~ m/\S/ ) ) {
next;
}
#guess file type from first line
if ( $line =~ m/^LOCUS\s+/ ) {
$options->{'type'} = "genbank";
}
elsif ( $line =~ m/^ID\s+/ ) {
$options->{'type'} = "embl";
}
elsif ( $line =~ m/^>/ ) {
$options->{'type'} = "fasta";
}
else {
$options->{'type'} = "raw";
}
last;
}
close(INFILE) or die("Cannot close input file: $!");
#get seqobj
my $in = Bio::SeqIO->new(
-format => $options->{'type'},
-file => $options->{'input'}
);
#merge multi-contig sequences
my @seqs = ();
while ( my $seq = $in->next_seq() ) {
push( @seqs, $seq );
}
Bio::SeqUtils->cat(@seqs);
return $seqs[0];
}
sub _usage {
print <<BLOCK;
sequence_to_multi_fasta.pl - split a DNA sequence.
DISPLAY HELP AND EXIT:
usage:
perl sequence_to_multi_fasta.pl -help
SPLIT DNA SEQUENCE:
usage:
perl sequence_to_multi_fasta.pl -i <file> -o <file> [Options]
required arguments:
-i - Input file in FASTA, RAW, EMBL, or GenBank format.
-o - Output file in FASTA format of sequence fragments.
optional arguments:
-v - The overlap to include between sequences, in bases. [Integer].
-s - The size of the sequences to create, in bases. [Integer]. Default is to
return the entire sequence as a single FASTA record.
example usage:
perl sequence_to_multi_fasta.pl -i input.gbk -o output.fasta -s 10000 -v 500
BLOCK
}
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