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#
# BioPerl module for Bio::AlignIO
#
# based on the Bio::SeqIO module
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
#
# History
# September, 2000 AlignIO written by Peter Schattner
# POD documentation - main docs before the code
=head1 NAME
Bio::AlignIO - Handler for AlignIO Formats
=head1 SYNOPSIS
use Bio::AlignIO;
$inputfilename = "testaln.fasta";
$in = Bio::AlignIO->new(-file => $inputfilename ,
-format => 'fasta');
$out = Bio::AlignIO->new(-file => ">out.aln.pfam" ,
-format => 'pfam');
while ( my $aln = $in->next_aln() ) {
$out->write_aln($aln);
}
# OR
use Bio::AlignIO;
open MYIN,"testaln.fasta";
$in = Bio::AlignIO->newFh(-fh => \*MYIN,
-format => 'fasta');
open my $MYOUT, '>', 'testaln.pfam';
$out = Bio::AlignIO->newFh(-fh => $MYOUT,
-format => 'pfam');
# World's smallest Fasta<->pfam format converter:
print $out $_ while <$in>;
=head1 DESCRIPTION
L<Bio::AlignIO> is a handler module for the formats in the AlignIO set,
for example, L<Bio::AlignIO::fasta>. It is the officially sanctioned way
of getting at the alignment objects. The resulting alignment is a
L<Bio::Align::AlignI>-compliant object.
The idea is that you request an object for a particular format.
All the objects have a notion of an internal file that is read
from or written to. A particular AlignIO object instance is configured
for either input or output, you can think of it as a stream object.
Each object has functions:
$stream->next_aln();
And:
$stream->write_aln($aln);
Also:
$stream->type() # returns 'INPUT' or 'OUTPUT'
As an added bonus, you can recover a filehandle that is tied to the
AlignIO object, allowing you to use the standard E<lt>E<gt> and print
operations to read and write alignment objects:
use Bio::AlignIO;
# read from standard input
$stream = Bio::AlignIO->newFh(-format => 'Fasta');
while ( $aln = <$stream> ) {
# do something with $aln
}
And:
print $stream $aln; # when stream is in output mode
L<Bio::AlignIO> is patterned on the L<Bio::SeqIO> module and shares
most of its features. One significant difference is that
L<Bio::AlignIO> usually handles IO for only a single alignment at a time,
whereas L<Bio::SeqIO> handles IO for multiple sequences in a single stream.
The principal reason for this is that whereas simultaneously handling
multiple sequences is a common requirement, simultaneous handling of
multiple alignments is not. The only current exception is format
C<bl2seq> which parses results of the BLAST C<bl2seq> program and which
may produce several alignment pairs. This set of alignment pairs can
be read using multiple calls to L<next_aln>.
=head1 CONSTRUCTORS
=head2 Bio::AlignIO-E<gt>new()
$seqIO = Bio::AlignIO->new(-file => 'filename', -format=>$format);
$seqIO = Bio::AlignIO->new(-fh => \*FILEHANDLE, -format=>$format);
$seqIO = Bio::AlignIO->new(-format => $format);
$seqIO = Bio::AlignIO->new(-fh => \*STDOUT, -format => $format);
The L<new> class method constructs a new L<Bio::AlignIO> object.
The returned object can be used to retrieve or print alignment
objects. L<new> accepts the following parameters:
=over 4
=item -file
A file path to be opened for reading or writing. The usual Perl
conventions apply:
'file' # open file for reading
'>file' # open file for writing
'>>file' # open file for appending
'+<file' # open file read/write
'command |' # open a pipe from the command
'| command' # open a pipe to the command
=item -fh
You may provide new() with a previously-opened filehandle. For
example, to read from STDIN:
$seqIO = Bio::AlignIO->new(-fh => \*STDIN);
Note that you must pass filehandles as references to globs.
If neither a filehandle nor a filename is specified, then the module
will read from the @ARGV array or STDIN, using the familiar E<lt>E<gt>
semantics.
=item -format
Specify the format of the file. Supported formats include:
bl2seq Bl2seq Blast output
clustalw clustalw (.aln) format
emboss EMBOSS water and needle format
fasta FASTA format
maf Multiple Alignment Format
mase mase (seaview) format
mega MEGA format
meme MEME format
msf msf (GCG) format
nexus Swofford et al NEXUS format
pfam Pfam sequence alignment format
phylip Felsenstein PHYLIP format
prodom prodom (protein domain) format
psi PSI-BLAST format
selex selex (hmmer) format
stockholm stockholm format
Currently only those formats which were implemented in L<Bio::SimpleAlign>
have been incorporated into L<Bio::AlignIO>. Specifically, C<mase>, C<stockholm>
and C<prodom> have only been implemented for input. See the specific module
(e.g. L<Bio::AlignIO::prodom>) for notes on supported versions.
If no format is specified and a filename is given, then the module
will attempt to deduce it from the filename suffix. If this is unsuccessful,
C<fasta> format is assumed.
The format name is case insensitive; C<FASTA>, C<Fasta> and C<fasta> are
all treated equivalently.
=back
=head2 Bio::AlignIO-E<gt>newFh()
$fh = Bio::AlignIO->newFh(-fh => \*FILEHANDLE, -format=>$format);
# read from STDIN or use @ARGV:
$fh = Bio::AlignIO->newFh(-format => $format);
This constructor behaves like L<new>, but returns a tied filehandle
rather than a L<Bio::AlignIO> object. You can read sequences from this
object using the familiar E<lt>E<gt> operator, and write to it using
L<print>. The usual array and $_ semantics work. For example, you can
read all sequence objects into an array like this:
@sequences = <$fh>;
Other operations, such as read(), sysread(), write(), close(), and printf()
are not supported.
=over 1
=item -flush
By default, all files (or filehandles) opened for writing alignments
will be flushed after each write_aln() making the file immediately
usable. If you do not need this facility and would like to marginally
improve the efficiency of writing multiple sequences to the same file
(or filehandle), pass the -flush option '0' or any other value that
evaluates as defined but false:
my $clustal = Bio::AlignIO->new( -file => "<prot.aln",
-format => "clustalw" );
my $msf = Bio::AlignIO->new(-file => ">prot.msf",
-format => "msf",
-flush => 0 ); # go as fast as we can!
while($seq = $clustal->next_aln) { $msf->write_aln($seq) }
=back
=head1 OBJECT METHODS
See below for more detailed summaries. The main methods are:
=head2 $alignment = $AlignIO-E<gt>next_aln()
Fetch an alignment from a formatted file.
=head2 $AlignIO-E<gt>write_aln($aln)
Write the specified alignment to a file..
=head2 TIEHANDLE(), READLINE(), PRINT()
These provide the tie interface. See L<perltie> for more details.
=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 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Peter Schattner
Email: schattner@alum.mit.edu
=head1 CONTRIBUTORS
Jason Stajich, jason@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::AlignIO;
use strict;
use Bio::Seq;
use Bio::LocatableSeq;
use Bio::SimpleAlign;
use Bio::Tools::GuessSeqFormat;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : $stream = Bio::AlignIO->new(-file => $filename,
-format => 'Format')
Function: Returns a new seqstream
Returns : A Bio::AlignIO::Handler initialised with
the appropriate format
Args : -file => $filename
-format => format
-fh => filehandle to attach to
-displayname_flat => 1 [optional]
to force the displayname to not show start/end
information
=cut
sub new {
my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::AlignIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{-file} || $ARGV[0] );
unless ($format) {
if ($param{-file}) {
$format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file}||$ARGV[0] )->guess;
}
elsif ($param{-fh}) {
$format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh}||$ARGV[0] )->guess;
}
}
$format = "\L$format"; # normalize capitalization to lower case
$class->throw("Unknown format given or could not determine it [$format]")
unless $format;
return unless( $class->_load_format_module($format) );
return "Bio::AlignIO::$format"->new(@args);
}
}
=head2 newFh
Title : newFh
Usage : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format')
$sequence = <$fh>; # read a sequence object
print $fh $sequence; # write a sequence object
Returns : filehandle tied to the Bio::AlignIO::Fh class
Args :
=cut
sub newFh {
my $class = shift;
return unless my $self = $class->new(@_);
return $self->fh;
}
=head2 fh
Title : fh
Usage : $obj->fh
Function:
Example : $fh = $obj->fh; # make a tied filehandle
$sequence = <$fh>; # read a sequence object
print $fh $sequence; # write a sequence object
Returns : filehandle tied to the Bio::AlignIO::Fh class
Args :
=cut
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
=head2 format
Title : format
Usage : $format = $stream->format()
Function: Get the alignment format
Returns : alignment format
Args : none
=cut
# format() method inherited from Bio::Root::IO
# _initialize is where the heavy stuff will happen when new is called
sub _initialize {
my($self,@args) = @_;
my ($flat,$alphabet,$width) = $self->_rearrange([qw(DISPLAYNAME_FLAT ALPHABET WIDTH)],
@args);
$self->force_displayname_flat($flat) if defined $flat;
$self->alphabet($alphabet);
$self->width($width) if defined $width;
$self->_initialize_io(@args);
1;
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL AlignIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::AlignIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the AlignIO system please see the AlignIO docs.
This includes ways of checking for formats at compile time, not run time
END
;
return;
}
return 1;
}
=head2 next_aln
Title : next_aln
Usage : $aln = stream->next_aln
Function: reads the next $aln object from the stream
Returns : a Bio::Align::AlignI compliant object
Args :
=cut
sub next_aln {
my ($self,$aln) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::AlignIO object.");
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln($aln)
Function: writes the $aln object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
=cut
sub write_aln {
my ($self,$aln) = @_;
$self->throw("Sorry, you cannot write to a generic Bio::AlignIO object.");
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'clustalw' if /\.aln$/i;
return 'emboss' if /\.(water|needle)$/i;
return 'metafasta' if /\.metafasta$/;
return 'fasta' if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i;
return 'maf' if /\.maf/i;
return 'mega' if /\.(meg|mega)$/i;
return 'meme' if /\.meme$/i;
return 'msf' if /\.(msf|pileup|gcg)$/i;
return 'nexus' if /\.(nexus|nex)$/i;
return 'pfam' if /\.(pfam|pfm)$/i;
return 'phylip' if /\.(phylip|phlp|phyl|phy|ph)$/i;
return 'psi' if /\.psi$/i;
return 'stockholm' if /\.stk$/i;
return 'selex' if /\.(selex|slx|selx|slex|sx)$/i;
return 'xmfa' if /\.xmfa$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my $class = shift;
return bless {'alignio' => shift},$class;
}
sub READLINE {
my $self = shift;
return $self->{'alignio'}->next_aln() unless wantarray;
my (@list,$obj);
push @list,$obj while $obj = $self->{'alignio'}->next_aln();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'alignio'}->write_aln(@_);
}
=head2 force_displayname_flat
Title : force_displayname_flat
Usage : $obj->force_displayname_flat($newval)
Function:
Example :
Returns : value of force_displayname_flat (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub force_displayname_flat{
my $self = shift;
return $self->{'_force_displayname_flat'} = shift if @_;
return $self->{'_force_displayname_flat'} || 0;
}
=head2 alphabet
Title : alphabet
Usage : $obj->alphabet($newval)
Function: Get/Set alphabet for purpose of passing to Bio::LocatableSeq creation
Example : $obj->alphabet('dna');
Returns : value of alphabet (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub alphabet {
my $self = shift;
my $value = shift;
if ( defined $value ) {
$self->throw("Invalid alphabet $value") unless $value eq 'rna' || $value eq 'protein' || $value eq 'dna';
$self->{'_alphabet'} = $value;
}
return $self->{'_alphabet'};
}
1;
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