# $Id: IO.pm 16690 2010-01-14 07:27:29Z kortsch $
#
# BioPerl module for Bio::Assembly::IO
#
# based on the Bio::SeqIO module
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# Copyright Robson Francisco de Souza
#
# You may distribute this module under the same terms as perl itself
#
# _history
# POD documentation - main docs before the code
=head1 NAME
Bio::Assembly::IO - Handler for Assembly::IO Formats
=head1 SYNOPSIS
use Bio::Assembly::IO;
$in = Bio::Assembly::IO->new(-file=>"<inputfilename",
-format=>'phrap');
$out = Bio::Assembly::IO->new(-file=>">outputfilename",
-format=>'phrap');
while ( my $scaffold = $in->next_assembly() ) {
# do something with Bio::Assembly::Scaffold instance
# ...
$out->write_assembly(-scaffold => $scaffold);
}
$in->close;
$out->close;
=head1 DESCRIPTION
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
(e.g. Bio::Assembly::IO::phrap).
=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 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
=head1 CONTRIBUTORS
#
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Assembly::IO;
use strict;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : $stream = Bio::Assembly::IO->new( -file => $filename,
-format =>'format' )
Function: Returns a new assembly stream
Returns : A Bio::Assembly::IO::Handler initialised
with the appropriate format
Args : -file => $filename
-format => format
=cut
sub new {
my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
$class->throw("Need at least a file name to proceed!")
unless (defined $param{'-file'} || defined $ARGV[0]);
my $format = $param{'-format'} ||
$class->_guess_format( $param{-file} || $ARGV[0] );
$format = "\L$format"; # normalize capitalization to lower case
if ($format =~ /-/) {
($format, my $variant) = split('-', $format, 2);
push @args, (-variant => $variant);
}
return unless( $class->_load_format_module($format) );
return "Bio::Assembly::IO::$format"->new(@args);
}
}
=head2 format
Title : format
Usage : $format = $stream->format()
Function: Get the assembly format
Returns : assembly format
Args : none
=cut
# format() method inherited from Bio::Root::IO
# _initialize is chained for all SeqIO classes
sub _initialize {
my($self, @args) = @_;
# initialize the IO part
$self->_initialize_io(@args);
}
=head2 next_assembly
Title : next_assembly
Usage : $scaffold = $stream->next_assembly()
Function: Reads the next assembly object from the stream and returns it.
Returns : a Bio::Assembly::ScaffoldI compliant object
Args : none
=cut
sub next_assembly {
my ($self) = @_;
$self->throw("Cannot read from a generic Bio::Assembly::IO object.");
}
=head2 next_contig
Title : next_contig
Usage : $contig = $stream->next_contig()
Function: Reads the next contig or singlet from the stream and returns it.
Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet
Args : none
=cut
sub next_contig {
my ($self) = @_;
$self->throw("Cannot read from a generic Bio::Assembly::IO object.");
}
=head2 write_assembly
Title : write_assembly
Usage : $stream->write_assembly($assembly)
Function: Write the assembly object in desired format. This method calls
write_header(), write_contigs() and write_footer() internally.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object
=cut
sub write_assembly {
my ($self, @args) = @_;
my ($scaf, $write_singlets) = $self->_rearrange([qw(SCAFFOLD SINGLETS)], @args);
# Sanity check
if ( !$scaf || !$scaf->isa('Bio::Assembly::ScaffoldI') ) {
$self->throw("Must provide a Bio::Assembly::Scaffold object when calling write_assembly");
}
# Write header
$self->write_header($scaf);
# ID-sorted contig and read entries
my @contig_ids = $scaf->get_contig_ids;
if ($write_singlets) {
push @contig_ids, $scaf->get_singlet_ids;
}
@contig_ids = _sort(@contig_ids);
# Write contigs
for my $contig_id ( @contig_ids ) {
my $contig = $scaf->get_contig_by_id($contig_id) ||
$scaf->get_singlet_by_id($contig_id);
$self->write_contig($contig);
}
# Write footer
$self->write_footer($scaf);
return 1;
}
=head2 write_header
Title : write_header
Usage : $stream->write_header($assembly)
Function: Write the start of the assembly file. It can be called at any time,
not when starting to write the assembly file.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object or ... (check the specific format
driver for more details)
=cut
sub write_header {
my ($self) = @_;
$self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
=head2 write_contig
Title : write_contig
Usage : $stream->write_contig($contig)
Function: Write a contig object in the desired format.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Contig object
=cut
sub write_contig {
my ($self) = @_;
$self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
=head2 write_footer
Title : write_footer
Usage : $stream->write_footer($assembly)
Function: Write the start of the assembly file.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object or ... (check the specific format
driver for more details)
=cut
sub write_footer {
my ($self) = @_;
$self->throw("Cannot write from a generic Bio::Assembly::IO object.");
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL Assembly::IO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::Assembly::IO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: could not load $format - for more details on supported formats please see the Assembly::IO docs
Exception $@
END
;
}
return $ok;
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function: guess format based on file suffix
Example :
Returns : guessed format of filename (lower case)
Args :
Notes : formats that _filehandle() will guess includes
ace, phrap and tigr at the moment
=cut
sub _guess_format {
my $class = shift;
my $arg = shift;
return unless defined($arg);
return 'ace' if ($arg =~ /\.ace/i);
return 'phrap' if ($arg =~ /\.phrap/i);
return 'tigr' if ($arg =~ /\.tigr/i);
return 'maq' if ($arg =~ /\.maq/i);
return 'sam' if ($arg =~ /\.[bs]am/i);
return 'bowtie' if ($arg =~ /\.bowtie/i);
}
=head2 _sort
Title : _sort
Usage : @sorted_values = $ass_io->_sort(@values)
Function: Sort a list of values naturally if Sort::Naturally is installed
(nicer), lexically otherwise (not as nice, but safe)
Returns : array of sorted values
Args : array of values to sort
=cut
sub _sort {
my @arr = @_;
my @sorted_arr;
if (eval { require Sort::Naturally }) {
@sorted_arr = Sort::Naturally::nsort( @arr ); # natural sort (better)
} else {
@sorted_arr = sort @arr; # lexical sort (safe)
}
return @sorted_arr;
}
sub DESTROY {
my $self = shift;
$self->close();
}
# I need some direction on these!! The module works so I haven't fiddled with them!
# Me neither! (rfsouza)
sub TIEHANDLE {
my ($class,$val) = @_;
return bless {'seqio' => $val}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'seqio'}->next_seq() || undef unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'seqio'}->next_seq();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'seqio'}->write_seq(@_);
}
1;