# $Id: fasta.pm 14669 2008-04-22 21:03:23Z cjfields $
# BioPerl module for Bio::SeqIO::fasta
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@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::fasta - 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.
=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@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - 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.open-bio.org/
=head1 AUTHORS - Ewan Birney & Lincoln Stein
Email: birney@ebi.ac.uk
lstein@cshl.org
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
=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::fasta;
use vars qw($WIDTH @SEQ_ID_TYPES $DEFAULT_SEQ_ID_TYPE);
use strict;
use Bio::Seq::SeqFactory;
use Bio::Seq::SeqFastaSpeedFactory;
use base qw(Bio::SeqIO);
@SEQ_ID_TYPES = qw(accession accession.version display primary);
$DEFAULT_SEQ_ID_TYPE = 'display';
BEGIN { $WIDTH = 60}
sub _initialize {
my($self,@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>";
return unless my $entry = $self->_readline;
chomp($entry);
if ($entry =~ m/\A\s*\Z/s) { # very first one
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 =~ tr/ \t\n\r//d; # 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
$alphabet = "dna";
}
} else {
# we don't need it really, so disable
# we want to keep this if SeqIO alphabet was set by user
# not sure if this could break something
#$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 $alphabet ) {
# don't assume that all our seqs are the same as the first one found
#$self->alphabet($seq->alphabet());
#}
return $seq;
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more Bio::PrimarySeqI objects
=cut
sub write_seq {
my ($self,@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 $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 defined $seq->display_id && $seq->display_id =~ /\s/;
$top = $seq->display_id();
$top = '' unless defined $top;
$self->warn("No whitespace allowed in FASTA ID [". $top. "]")
if defined $top && $top =~ /\s/;
} elsif($id_type =~ /^pri/i ) {
$top = $seq->primary_id();
}
if ($seq->can('desc') and my $desc = $seq->desc()) {
$desc =~ s/\n//g;
$top .= " $desc";
}
if( $seq->isa('Bio::Seq::LargeSeqI') ) {
$self->_print(">$top\n");
# for large seqs, don't call seq(), it defeats the
# purpose of the largeseq functionality. instead get
# chunks of the seq, $width at a time
my $buff_max = 2000;
my $buff_size = int($buff_max/$width)*$width; #< buffer is even multiple of widths
my $seq_length = $seq->length;
my $num_chunks = int($seq_length/$buff_size+1);
for( my $c = 0; $c < $num_chunks; $c++ ) {
my $buff_end = $buff_size*($c+1);
$buff_end = $seq_length if $buff_end > $seq_length;
my $buff = $seq->subseq($buff_size*$c+1,$buff_end);
if($buff) {
$buff =~ s/(.{1,$width})/$1\n/g;
$self->_print($buff);
} else {
$self->_print("\n");
}
}
} else {
my $str = $seq->seq;
if(defined $str && length($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;
}
1;