.travis.yml

-language: perl
-perl:
-  - "5.26"
-  - "5.24"
-  - "5.20"
-  - "5.18"
-  - "5.16"
-
-matrix:
-  include:
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=1
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=2
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=3
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=4
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=5
-    - perl: 5.18
-      env: COVERAGE=1 TEST_PARTITION=6
-
-sudo: false
-env:
-  global:
-    - PERL_CPANM_OPT="--notest --force --skip-satisfied"
-    - BIOPERL_NETWORK_TESTING=0   # disables the network tests
-    - TEST_PARTITIONS=6
-
-addons:
-  apt:
-    packages:
-      - libdb-dev
-      - graphviz
-      - libgd2-xpm-dev
-      - libxml2-dev
-
-before_install:
-  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
-  - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
-  - source ~/travis-perl-helpers/init
-  - build-perl
-  - perl -V
-  - cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1
-  - cpanm Test::Pod 2>&1 | tail -n 1
-  - cpanm Bio::ASN1::EntrezGene 2>&1 | tail -n 1
-  - if [ "$TRAVIS_EVENT_TYPE" = "cron" -a "$BRANCH" = "network-cron-master" ]; then
-      export BIOPERL_NETWORK_TESTING=1;
-      git fetch origin master:master; git checkout master;
-    fi
-  - if [ "$BIOPERL_NETWORK_TESTING" = "1" ]; then
-      export TRAVIS_AUTHOR_TESTING=1;
-      export TRAVIS_RELEASE_TESTING=1;
-      cpanm LWP::UserAgent LWP::Protocol::https 2>&1 | tail -n 1;
-    fi
-  - build-dist
-  - cd $BUILD_DIR
-install:
-  - cpan-install --deps
-  - cpan-install --coverage
-before_script:
-  - coverage-setup
-script:
-  - export AUTHOR_TESTING=${TRAVIS_AUTHOR_TESTING:=0}
-  - export RELEASE_TESTING=${TRAVIS_RELEASE_TESTING:=0}
-  - prove -l -j$(test-jobs) $(test-files)
-after_success:
-  - coverage-report
-  - ./travis_scripts/trigger-dockerhub.sh
-
-#TODO - send emails to bioperl-guts-l
-notifications:
-  email:
-    recipients:
-      - bioperl-guts-l@lists.open-bio.org
-      - cjfields1@gmail.com
-    on_success: change
-    on_failure: change
-
-# whitelist branches
-branches:
-  only:
-    - master
-    - /^release-[1-9]*-[0-9]*-[0-9]*$/
-    - network-cron-master

AUTHORS

@@ -14,7 +14,7 @@
 
 =item * Hilmar Lapp <hlapp at gmx.net>
 
-=item * Heikki Lehvslaiho <heikki at ebi.ac.uk>
+=item * Heikki Lehväslaiho <heikki at ebi.ac.uk>
 
 =item * Aaron Mackey <amackey at pcbi.upenn.edu>
 
@@ -145,7 +145,7 @@ for if you see fit)
 
 =item * Arek Kasprzyk <arek at ebi.ac.uk>
 
-=item * Andreas Khri <andreas.kahari at ebi.ac.uk>
+=item * Andreas Kähäri <andreas.kahari at ebi.ac.uk>
 
 =item * Charles C. Kim <cckim at stanford.edu>
 

BUGS

-# $Id: BUGS,v 1.7 2006-11-16 10:51:50 sendu Exp $
-
-Known Bugs
-
-Bugs are tracked at this URL:
-https://github.com/bioperl/bioperl-live/issues
-
-Bioperl 1.6 series
-=============
-
-Though a stable release, some bugs and enhancements remain for this series
-that will be addressed in future point releases. For a full list please see:
-
-https://github.com/bioperl/bioperl-live/issues
-
-Bug     Summary (additional info)
-
-2247    Have Bio::SearchIO::blast methods available for other BLAST parsers
-        (enhancement request)
-2332    Software for analysis of redundant fragments of affys human mitochip v2
-        (API hasn't stabilized, may appear in a 1.6 point release)
-2439    multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO
-        (partially implemented)
-2463    bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface
-        (enhancement request)
-2476    "Undefined sub-sequence" when processing tblastx output
-        (related to HSP tiling)
-2482    paml4 mlc file fails to parse
-        (may require refactoring Bio::Tools::Phylo::PAML)
-2492    Method "pi" in package Bio::PopGen::Statistics
-        (awaiting comment from Jason)
-2513    creating a Bio::SeqFeature::Annotation object downloads the entire so.obo
-        (should allow local copies)
-2594    Bio::Species memory leak
-        (fix implemented, but additional leaks likely remain)
-2673    original fields not inherited by seq objects in alignment slices
-        (request for bequest/bequeath behavior for attribute carryover)
-2686    WU-BLAST XML support
-        (partially implemented, but issues remain)
-2691    Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency
-        (related to bug 2332 above)
-2696    global verbosity does not propagate to new objects post-set
-        (requires more specific implementation details)
-2700    Refactor Build.PL
-        (some of the behind-the-scenes stuff is a little klunky)
-2702    Scripts recopied upon each call to './Build test'
-        (minor bug)
-2703    Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP
-        (minor bug that mistakes format)
-2707    Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in
-        filenames, but Bio::SearchIO::blast does
-        (bug within StandAloneBlast)
-2715    LocatableSeq symbols are globally set
-        (bug related to sequence symbol issues; rarely surfaces but needs addressing)
-
-
-Bioperl 1.5.2
-=============
-
-There are no known installation bugs in 1.5.2 per se, but issues with
-external programs may cause problems. See the following URL for details:
-http://www.bioperl.org/wiki/Release_1.5.2#Notes
-
-
-Bioperl 1.2
-===========
-
- * The StandAloneBlast.t test is failing on cygwin installations (and
-   nowhere else). We suspect something to do with temporary file
-   opening. Fixed in 1.4 (set TMPDIR).
-
-
-Bioperl 0.9.0 
-=============
-
- * Bio::Tools::Blast continues to cause problems for some people.  As
-   it is not actively maintained there are a slew of reported bugs for 
-   it that have not been fixed.  
-
- * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get 
-   all parameters it needs when aligning (two) two DNA sequences
-   (jitterbug #966).
-
- * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for
-   clustalw versions 1.8x due to a bug in clustalw.
-
- * Bio::DB::GenBank continues to have intermittent errors.  Bio::DB::GDB 
-   is also unreliable at times and one can safely ignore errors from
-   these during a make test.  
-   Bio::DB::GenBank is unable to download whole contig files as well
-   as NCBI ref seqs like NT_* numbers unless the -format flag is
-   passed in and specified as 'fasta' in the constructor.
-   get_Stream_by_batch() also has intermittent errors which are being
-   tracked down.
-
-
-Bioperl 0.7.2
-=============
-
- * NCBI has changed some of the cgi scripts for retrieving sequences
-   online which as resulted in some of the DB methods from not working
-   consistently.  We are addressing these in the 0.9.x and 1.0 series
-   of releases.  We recommend using the Bio::DB::EMBL object that is
-   part of the later releases. 
- 
-   Additionally RefSeq Contigs are not properly downloaded, please see
-   the bioperl list archives for information about potential
-   workarounds and ongoing development effort to address these.
-
-
-Bioperl 0.7.1
-=============
-
- * Bio::Tools::BPlite does not parse and set frame properly for
-   tblastx reports (Jitterbug bug # 978).
-
- * Bio::Tools::BPlite interface needs to be updated to fix parsing
-   more than bl2seq report report (Jitterbug bug #940), this has been
-   fixed on the main code trunk and will be part of the next major
-   bioperl release.
- 
- * If File::Temp is not installed, tempdirs are not cleaned up
-   properly.  This is fixed on main code trunk with the introduction
-   of rmtree method in Bio::Root::IO, however, it is best to install
-   File::Temp when running 0.7 branch code.
- 
- * Bio::Tools::Blast does not allow users to run blast, instead use
-   Bio::Tools::Run::StandAloneBlast to run local blasts.  To submit
-   jobs to a remote blast server like NCBI a module
-   Bio::Tools::Run::RemoteBlast has been written but is part of the
-   main trunk code and must be obtained through CVS until the next
-   major bioperl release.
-
-
-Bioperl 0.7
-===========
-
- * Bio::Tools::BPlite doc error lists
-   code synopsis code as 
-     my $parser = new BPlite(\*FH);  
-   should be 
-     my $parser = new Bio::Tools::BPlite(\*FH);
-  

Bio/AlignIO/nexml.pm

-#
-# BioPerl module for Bio::AlignIO::nexml
-#
-# Copyright Chase Miller
-#
-# You may distribute this module under the same terms as perl itself
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
-
-=head1 SYNOPSIS
-
-Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
-
-=head1 DESCRIPTION
-
-This object can transform L<Bio::SimpleAlign> objects to and from
-NeXML format. For more information on NeXML, visit L<http://www.nexml.org>.
-
-=head1 FEEDBACK
-
-=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 AUTHORS
-
-Chase Miller
-
-=head1 CONTRIBUTORS
-
-Mark Jensen, maj@fortinbras.us
-Rutger Vos, rutgeraldo@gmail.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::AlignIO::nexml;
-
-use strict;
-use lib '../..';
-use Bio::Nexml::Factory;
-use Bio::Phylo::IO qw(parse unparse);
-
-use base qw(Bio::AlignIO);
-
-
-sub _initialize {
-  my($self,@args) = @_;
-  $self->SUPER::_initialize(@args);  
-  $self->{_doc} = undef;
-}
-
-=head2 next_aln
-
- Title   : next_aln
- Usage   : $aln = $stream->next_aln
- Function: returns the next alignment in the stream.
- Returns : Bio::Align::AlignI object - returns 0 on end of file
-	        or on error
- Args    : 
-
-See L<Bio::Align::AlignI>
-
-=cut
-
-sub next_aln {
-	my ($self) = @_;
-    unless ( $self->{'_parsed'} ) {
-    	#use a parse function to load all the alignment objects found in the nexml file at once
-        $self->_parse;
-    }
-    return $self->{'_alns'}->[ $self->{'_alnsiter'}++ ];
-}
-
-=head2 rewind
-
- Title   : rewind
- Usage   : $alnio->rewind
- Function: Resets the stream
- Returns : none
- Args    : none
-
-
-=cut
-
-sub rewind {
-    my $self = shift;
-    $self->{'_alniter'} = 0;
-}
-
-=head2 doc
-
- Title   : doc
- Usage   : $treeio->doc
- Function: Returns the biophylo nexml document object
- Returns : Bio::Phylo::Project
- Args    : none or Bio::Phylo::Project object
-
-=cut
-
-sub doc {
-	my ($obj,$value) = @_;
-   if( defined $value) {
-      $obj->{'_doc'} = $value;
-	}
-	return $obj->{'_doc'};
-}
-
-sub _parse {
-    my ($self) = @_;
-
-    $self->{'_parsed'}   = 1;
-    $self->{'_alnsiter'} = 0;
-    my $fac = Bio::Nexml::Factory->new();
-
-    # Only pass filename if filehandle is not available,
-    # or "Bio::Phylo" will create a new filehandle that ends
-    # out of scope and can't be closed directly, leaving 2 open
-    # filehandles for the same file (so file can't be deleted)
-    my $file_arg;
-    my $file_value;
-    if (     exists $self->{'_filehandle'}
-        and defined $self->{'_filehandle'}
-        ) {
-        $file_arg   = '-handle';
-        $file_value = $self->{'_filehandle'};
-    }
-    else {
-        $file_arg   = '-file';
-        $file_value = $self->{'_file'};
-    }
-
-    $self->doc(parse(
-                     $file_arg     => $file_value,
-                     '-format'     => 'nexml',
-                     '-as_project' => '1'
-                     )
-    );
-    $self->{'_alns'} = $fac->create_bperl_aln($self);
-
-    if(@{ $self->{'_alns'} } == 0) {
-        self->debug("no seqs in $self->{_file}");
-    }
-}
-
-=head2 write_aln
-
- Title   : write_aln
- Usage   : $stream->write_aln(@aln)
- Function: writes the $aln object into the stream in nexml format
- Returns : 1 for success and 0 for error
- Args    : L<Bio::Align::AlignI> object
-
-See L<Bio::Align::AlignI>
-
-=cut
-
-sub write_aln {
-	my ($self, $aln) = @_;
-	
-    my $fac = Bio::Nexml::Factory->new();
-    my $taxa = $fac->create_bphylo_taxa($aln);
-	my ($matrix) = $fac->create_bphylo_aln($aln, $taxa);
-	$matrix->set_taxa($taxa);
-	
-	$self->doc(Bio::Phylo::Factory->create_project());
-	$self->doc->insert($matrix);
-	my $ret = $self->_print($self->doc->to_xml());
-	$self->flush;
-	return $ret;
-}
-
-
-
-
-
-
-
-
-1;

Bio/Assembly/IO.pm

-# $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;