[Bioperl-l] Bio::SeqIO::multifasta
Jean-Marc Frigerio
Frigerio at pierroton.inra.fr
Thu Feb 24 11:05:13 EST 2005
Hi,
I slightly modified the Bio::SeqIO::fasta module in order to be able to
navigate in the fasta file, by in-memory indexing (not in-file indexing like
Bio::Index::Fasta).
I added the get_by_id(), get_by_order(), first_seq() and previous_seq()
methods and a few internal ones.
You can test it by copying the following code in your Bio/SeqIO/ directory
and then use it like this :
----------------------------------------------------------------------------
#! /usr/bin/env perl
use strict;
use warnings;
# vim: fdm=marker fdl=0 fdc=2 fmr=/*,*/
#
use Bio::SeqIO;
my $seqio = Bio::SeqIO->new (-file => $ARGV[0] , '-format' => 'multifasta');
print "10th "$seqio->get_by_order(10)->id,"\n";
print "11th ",$seqio->next_seq->id,"\n";
print "10th ", $seqio->previous_seq->id,"\n";
This module is usefull for me, I hope it will be for others, I'm also willing
to improve my perl so please criticize.
--- Jean-Marc
--------------------------------------------------------------------------------------------
On my box /usr/lib/perl5/site_perl/5.8.1/Bio/SeqIO/multifasta.pm
--------------------------------------------------------------------------------------------
# $Id: multifasta.pm $
# BioPerl module for Bio::SeqIO::multifasta
#
# Cared for by Ewan Birney <birney at ebi.ac.uk>
# and Lincoln Stein <lstein at cshl.org>
#
# Copyright Ewan Birney & Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
# _history
# October 18, 1999 Largely rewritten by Lincoln Stein
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::multifasta - fasta sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from fasta flat
file databases.
Added the get_by_id(), get_by_order(), first_seq() and previous_seq() methods
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l at bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.bioperl.org/
=head1 AUTHORS - Ewan Birney & Lincoln Stein
Email: birney at ebi.ac.uk
lstein at cshl.org
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
Jean-Marc Frigerio, Frigerio at pierroton.inra.fr
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::multifasta;
use vars qw(@ISA $WIDTH @SEQ_ID_TYPES $DEFAULT_SEQ_ID_TYPE);
use strict;
# Object preamble - inherits from Bio::Root::Object
use Bio::SeqIO;
use Bio::Seq::SeqFactory;
use Bio::Seq::SeqFastaSpeedFactory;
@ISA = qw(Bio::SeqIO);
@SEQ_ID_TYPES = qw(accession accession.version display primary);
$DEFAULT_SEQ_ID_TYPE = 'display';
BEGIN { $WIDTH = 60}
sub _initialize {
my($self, at args) = @_;
$self->SUPER::_initialize(@args);
my ($width) = $self->_rearrange([qw(WIDTH)], @args);
$width && $self->width($width);
unless ( defined $self->sequence_factory ) {
$self->sequence_factory(Bio::Seq::SeqFastaSpeedFactory->new());
}
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
=cut
sub next_seq {
my( $self ) = @_;
my $seq;
my $alphabet;
local $/ = "\n>";
my $pos = $self->_position; #jmf
return unless my $entry = $self->_readline;
chomp($entry);
if ($entry =~ m/\A\s*\Z/s) { # very first one
my $pos = $self->_position; #jmf
return unless $entry = $self->_readline;
chomp($entry);
}
$entry =~ s/^>//;
my ($top,$sequence) = split(/\n/,$entry,2);
defined $sequence && $sequence =~ s/>//g;
# my ($top,$sequence) = $entry =~ /^>?(.+?)\n+([^>]*)/s
# or $self->throw("Can't parse fasta entry");
my ($id,$fulldesc);
if( $top =~ /^\s*(\S+)\s*(.*)/ ) {
($id,$fulldesc) = ($1,$2);
}
if (defined $id && $id eq '') {$id=$fulldesc;} # FIX incase no space
# between > and name \AE
defined $sequence && $sequence =~ s/\s//g; # Remove whitespace
# for empty sequences we need to know the mol.type
$alphabet = $self->alphabet();
if(defined $sequence && length($sequence) == 0) {
if(! defined($alphabet)) {
# let's default to dna
$alphabet = "dna";
}
} else {
# we don't need it really, so disable
$alphabet = undef;
}
$seq = $self->sequence_factory->create(
-seq => $sequence,
-id => $id,
# Ewan's note - I don't think this healthy
# but obviously to taste.
#-primary_id => $id,
-desc => $fulldesc,
-alphabet => $alphabet,
-direct => 1,
);
# if there wasn't one before, set the guessed type
unless ( defined $alphabet ) {
$self->alphabet($seq->alphabet());
}
$self->_push($seq->id,$pos);#jmf
return $seq;
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : array of 1 to n Bio::PrimarySeqI objects
=cut
sub write_seq {
my ($self, at seq) = @_;
my $width = $self->width;
foreach my $seq (@seq) {
$self->throw("Did not provide a valid Bio::PrimarySeqI object")
unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
my $str = $seq->seq;
my $top;
# Allow for different ids
my $id_type = $self->preferred_id_type;
if( $id_type =~ /^acc/i ) {
$top = $seq->accession_number();
if( $id_type =~ /vers/i ) {
$top .= "." . $seq->version();
}
} elsif($id_type =~ /^displ/i ) {
$self->warn("No whitespace allowed in FASTA ID [".
$seq->display_id. "]")
if $seq->display_id =~ /\s/;
$top = $seq->display_id();
} elsif($id_type =~ /^pri/i ) {
$top = $seq->primary_id();
}
if ($seq->can('desc') and my $desc = $seq->desc()) {
$desc =~ s/\n//g;
$top .= " $desc";
}
if(length($str) > 0) {
$str =~ s/(.{1,$width})/$1\n/g;
} else {
$str = "\n";
}
$self->_print (">",$top,"\n",$str) or return;
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 width
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for FASTA output
Returns : value of width
Args : newvalue (optional)
=cut
sub width{
my ($self,$value) = @_;
if( defined $value) {
$self->{'width'} = $value;
}
return $self->{'width'} || $WIDTH;
}
=head2 preferred_id_type
Title : preferred_id_type
Usage : $obj->preferred_id_type('accession')
Function: Get/Set the preferred type of identifier to use in the ">ID"
position
for FASTA output.
Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
Args : string when setting. This must be one of values defined in
@Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
accession, accession.version, display, primary
Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.
=cut
sub preferred_id_type {
my ($self,$type) = @_;
if( defined $type ) {
if( ! grep lc($type) eq $_, @SEQ_ID_TYPES) {
$self->throw(-class=>'Bio::Root::BadParameter',
-text=>"Invalid ID type \"$type\". Must be one of: @SEQ_ID_TYPES");
}
$self->{'_seq_id_type'} = lc($type);
# print STDERR "Setting preferred_id_type=$type\n";
}
$self->{'_seq_id_type'} || $DEFAULT_SEQ_ID_TYPE;
}
=head1 NEW METHODS (not in fasta.pm)
=cut
=head2 get_by_id
Title : get_by_id
Usage : $seqio->get_by_id('077F05');
Args : EST id
Returns : A Bio::Seq
=cut
sub get_by_id
{
my $self = shift;
my $id = shift || return;
if (defined $self->{IDS}{$id} )
{
$self->_position($id);
return $self->next_seq;
}
else
{
while (my $seq = $self->next_seq)
{
return $seq if $seq->id eq $id
}
}
}
=head2 get_by_order
Title : get_by_order
Usage : $seqio->get_by_order(10);
Args : a number
returns : a bio::seq
=cut
sub get_by_order
{
my ($self,$order) = @_;
$order--;
my $count = 0;
my $seq;
if ($order > $#{$self->{lIST}})
{
while ($seq = $self->next_seq)
{
return $seq if $order == $count++
}
seek( $self->_fh, $self->{LIST}[-1], 0);
return $self->next_seq;
}
else
{
seek( $self->_fh, $self->{LIST}[$order], 0);
return $self->next_seq;
}
}
=head2 first_seq
Title : first_seq
Usage : $seqio->first_seq;
Functions : "Rewind" the filehandle to the beginning of the file
Args : none
Returns : A Bio::Seq
=cut
sub first_seq
{
my $self = shift;
seek($self->_fh,0,0);
return $self->next_seq;
}
=head2 previous_seq
Title : first_seq
Usage : $seqio->first_seq;
Functions : "Rewind" the filehandle to the previous seq
Args : none
Returns : A Bio::Seq
=cut
sub previous_seq
{
my $self = shift;
seek($self->_fh,$self->{LIST}[-2],0);
return $self->next_seq;
}
=head1 PRIVATE METHODS
=head2 _position
Title : _position
Usage : $self->_position();
Function : Set/get the position in the file
Example : $self->_position($id);
Args : id (optional)
Returns : the current position in the file
=cut
sub _position
{
my $self = shift;
my $fh = $self->_fh;
if (@_)
{
my $id = shift;
seek($fh,$self->{IDS}{$id},0);
}
return tell $fh;
}
=head2 _push
Title : _push
Usage : $self->_push;
Function : Stores id and position in the hash $self->{IDS}
Example : $self->_push($next->id,$pos);
Args : id, position in the file
Returns : none
=cut
sub _push
{
my $self = shift;
my ($id,$pos) = @_;
$self->{IDS}{$id} = $pos;
push @{$self->{LIST}},$pos;
}
=head1 _pop_all
Title : _pop_all
Usage : $self->_pop_all;
Function : print the content of $self->{IDS}
Example : $self->_pop_all;
Args : none
Returns : none
=cut
sub _pop_all
{
my $self = shift;
for (keys %{$self->{IDS}})
{
print "$_ : $self->{IDS}{$_}\n";
}
}
1;
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