#
# BioPerl module for Bio::Structure::IO
#
# Copyright 2001, 2002 Kris Boulez
#
# You may distribute this module under the same terms as perl itself
#
# _history
# October 18, 1999 Largely rewritten by Lincoln Stein
# November 16, 2001 Copied Bio::SeqIO to Bio::Structure::IO and modified
# where needed. Factoring out common methods
# (to Bio::Root::IO) might be a good idea.
# POD documentation - main docs before the code
=head1 NAME
Bio::Structure::IO - Handler for Structure Formats
=head1 SYNOPSIS
use Bio::Structure::IO;
$in = Bio::Structure::IO->new(-file => "inputfilename",
-format => 'pdb');
while ( my $struc = $in->next_structure() ) {
print "Structure ", $struc->id, " number of models: ",
scalar $struc->model,"\n";
}
=head1 DESCRIPTION
Bio::Structure::IO is a handler module for the formats in the
Structure::IO set (e.g. L<Bio::Structure::IO::pdb>). It is the officially
sanctioned way of getting at the format objects, which most people
should use.
The Bio::Structure::IO system can be thought of like biological file
handles. They are attached to filehandles with smart formatting rules
(e.g. PDB format) and can either read or write structure objects
(Bio::Structure objects, or more correctly, Bio::Structure::StructureI
implementing objects, of which Bio::Structure is one such object). If
you want to know what to do with a Bio::Structure object, read
L<Bio::Structure>.
The idea is that you request a stream object for a particular format.
All the stream objects have a notion of an internal file that is read
from or written to. A particular Structure::IO object instance is
configured for either input or output. A specific example of a stream
object is the Bio::Structure::IO::pdb object.
Each stream object has functions
$stream->next_structure();
and
$stream->write_structure($struc);
also
$stream->type() # returns 'INPUT' or 'OUTPUT'
As an added bonus, you can recover a filehandle that is tied to the
Structure::IOIO object, allowing you to use the standard E<lt>E<gt>
and print operations to read and write structure::IOuence objects:
use Bio::Structure::IO;
$stream = Bio::Structure::IO->newFh(-format => 'pdb'); # read from standard input
while ( $structure = <$stream> ) {
# do something with $structure
}
and
print $stream $structure; # when stream is in output mode
=head1 CONSTRUCTORS
=head2 Bio::Structure::IO-E<gt>new()
$stream = Bio::Structure::IO->new(-file => 'filename', -format=>$format);
$stream = Bio::Structure::IO->new(-fh => \*FILEHANDLE, -format=>$format);
$stream = Bio::Structure::IO->new(-format => $format);
The new() class method constructs a new Bio::Structure::IO object. The
returned object can be used to retrieve or print Bio::Structure
objects. 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:
$strucIO = Bio::Structure::IO->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:
pdb Protein Data Bank format
If no format is specified and a filename is given, then the module
will attempt to deduce it from the filename. If this is unsuccessful,
PDB format is assumed.
The format name is case insensitive. 'PDB', 'Pdb' and 'pdb' are
all supported.
=back
=head2 Bio::Structure::IO-E<gt>newFh()
$fh = Bio::Structure::IO->newFh(-fh => \*FILEHANDLE, -format=>$format);
$fh = Bio::Structure::IO->newFh(-format => $format);
# etc.
This constructor behaves like new(), but returns a tied filehandle
rather than a Bio::Structure::IO object. You can read structures from this
object using the familiar E<lt>E<gt> operator, and write to it using
print(). The usual array and $_ semantics work. For example, you can
read all structure objects into an array like this:
@structures = <$fh>;
Other operations, such as read(), sysread(), write(), close(), and printf()
are not supported.
=head1 OBJECT METHODS
See below for more detailed summaries. The main methods are:
=head2 $structure = $structIO-E<gt>next_structure()
Fetch the next structure from the stream.
=head2 $structIO-E<gt>write_structure($struc [,$another_struc,...])
Write the specified structure(s) to the stream.
=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 AUTHORS - Ewan Birney, Lincoln Stein, Kris Boulez
Email birney@ebi.ac.uk, lstein@cshl.org, kris.boulez@algonomics.com
=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::Structure::IO;
use strict;
use Bio::PrimarySeq;
use Symbol;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : $stream = Bio::Structure::IO->new(-file => $filename, -format => 'Format')
Function: Returns a new structIOstream
Returns : A Bio::Structure::IO handler initialised with the appropriate format
Args : -file => $filename
-format => format
-fh => filehandle to attach to
=cut
my $entry = 0;
sub new {
my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::Structure::IO::(\S+)/ ) {
my ($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] ) ||
'pdb';
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return unless( &_load_format_module($format) );
return "Bio::Structure::IO::$format"->new(@args);
}
}
=head2 newFh
Title : newFh
Usage : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
$structure = <$fh>; # read a structure object
print $fh $structure; # write a structure object
Returns : filehandle tied to the Bio::Structure::IO::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
$structure = <$fh>; # read a structure object
print $fh $structure; # write a structure object
Returns : filehandle tied to the Bio::Structure::IO::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 = $obj->format()
Function: Get the structure format
Returns : structure format
Args : none
=cut
# format() method inherited from Bio::Root::IO
# _initialize is chained for all SeqIO classes
sub _initialize {
my($self, @args) = @_;
# not really necessary unless we put more in RootI
$self->SUPER::_initialize(@args);
# initialize the IO part
$self->_initialize_io(@args);
}
=head2 next_structure
Title : next_structure
Usage : $structure = stream->next_structure
Function: Reads the next structure object from the stream and returns a
Bio::Structure::Entry object.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2) (see
Bio::RootI POD page).
Returns : a Bio::Structure::Entry object
Args : none
=cut
sub next_structure {
my ($self, $struc) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::Structure::IO object.");
}
# Do we want people to read out the sequence directly from a $structIO stream
#
##=head2 next_primary_seq
##
## Title : next_primary_seq
## Usage : $seq = $stream->next_primary_seq
## Function: Provides a primaryseq type of sequence object
## Returns : A Bio::PrimarySeqI object
## Args : none
##
##
##=cut
##
##sub next_primary_seq {
## my ($self) = @_;
##
## # in this case, we default to next_seq. This is because
## # Bio::Seq's are Bio::PrimarySeqI objects. However we
## # expect certain sub classes to override this method to provide
## # less parsing heavy methods to retrieving the objects
##
## return $self->next_seq();
##}
=head2 write_structure
Title : write_structure
Usage : $stream->write_structure($structure)
Function: writes the $structure object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Structure object
=cut
sub write_seq {
my ($self, $struc) = @_;
$self->throw("Sorry, you cannot write to a generic Bio::Structure::IO object.");
}
# De we need this here
#
##=head2 alphabet
##
## Title : alphabet
## Usage : $self->alphabet($newval)
## Function: Set/get the molecule type for the Seq objects to be created.
## Example : $seqio->alphabet('protein')
## Returns : value of alphabet: 'dna', 'rna', or 'protein'
## Args : newvalue (optional)
## Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein'
##
##=cut
##
##sub alphabet {
## my ($self, $value) = @_;
##
## if ( defined $value) {
## # instead of hard-coding the allowed values once more, we check by
## # creating a dummy sequence object
## eval {
## my $seq = Bio::PrimarySeq->new('-alphabet' => $value);
## };
## if($@) {
## $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values.");
## }
## $self->{'alphabet'} = "\L$value";
## }
## return $self->{'alphabet'};
##}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL Structure::IO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($format) = @_;
my ($module, $load, $m);
$module = "_<Bio/Structure/IO/$format.pm";
$load = "Bio/Structure/IO/$format.pm";
return 1 if $main::{$module};
eval {
require $load;
};
if ( $@ ) {
print STDERR <<END;
$load: $format cannot be found
Exception $@
For more information about the Structure::IO system please see the
Bio::Structure::IO docs. This includes ways of checking for formats at
compile time, not run time
END
;
return;
}
return 1;
}
=head2 _concatenate_lines
Title : _concatenate_lines
Usage : $s = _concatenate_lines($line, $continuation_line)
Function: Private. Concatenates two strings assuming that the second stems
from a continuation line of the first. Adds a space between both
unless the first ends with a dash.
Takes care of either arg being empty.
Example :
Returns : A string.
Args :
=cut
sub _concatenate_lines {
my ($self, $s1, $s2) = @_;
$s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2);
return ($s1 ? $s1 : "") . ($s2 ? $s2 : "");
}
=head2 _filehandle
Title : _filehandle
Usage : $obj->_filehandle($newval)
Function: This method is deprecated. Call _fh() instead.
Example :
Returns : value of _filehandle
Args : newvalue (optional)
=cut
sub _filehandle {
my ($self,@args) = @_;
return $self->_fh(@args);
}
=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 $_ = shift;
return 'fasta' if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i;
return 'genbank' if /\.(gb|gbank|genbank)$/i;
return 'scf' if /\.scf$/i;
return 'pir' if /\.pir$/i;
return 'embl' if /\.(embl|ebl|emb|dat)$/i;
return 'raw' if /\.(txt)$/i;
return 'gcg' if /\.gcg$/i;
return 'ace' if /\.ace$/i;
return 'bsml' if /\.(bsm|bsml)$/i;
return 'pdb' if /\.(ent|pdb)$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my ($class,$val) = @_;
return bless {'structio' => $val}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'structio'}->next_seq() unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'structio'}->next_seq();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'structio'}->write_seq(@_);
}
1;