#
# BioPerl module for Bio::SeqIO::game::seqHandler
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sheldon McKay <mckays@cshl.edu>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequences
=head1 SYNOPSIS
This modules is not used directly
=head1 DESCRIPTION
Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record
and, via feature handlers, processes the associated annotations
=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
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sheldon McKay
Email mckays@cshl.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::SeqIO::game::seqHandler;
use Data::Dumper;
use Bio::SeqIO::game::featHandler;
use Bio::SeqFeature::Generic;
use Bio::Seq::RichSeq;
use Bio::Species;
use strict;
use vars qw {};
use base qw(Bio::SeqIO::game::gameSubs);
=head2 new
Title : new
Usage : my $seqHandler = Bio::SeqIO::game::seqHandler->new($seq, $ann, $comp, $map, $src )
Function: constructor method to create a sequence handler
Returns : a sequence handler object
Args : $seq -- an XML sequence element
$ann -- a ref. to a list of <annotation> elements
$comp -- a ref. to a list of <computational_analysis> elements (not used yet)
$map -- a <map_position> element
$src -- a flag to indicate that the sequence already has a source feature
=cut
sub new {
my ($caller, $seq, $ann, $comp, $map, $src ) = @_;
my $class = ref($caller) || $caller;
my $self = bless ( {
seqs => $seq,
anns => $ann,
comps => $comp,
map_pos => $map,
has_source => $src,
seq_h => {},
ann_l => []
}, $class );
return $self;
}
=head2 convert
Title : convert
Usage : @seqs = $seqHandler->convert
Function: converts the main XML sequence element and associated annotations to Bio::
Returns : a ref. to a an array containing the sequence object and a ref. to a list of features
Args : none
Note : The features and sequence are kept apart to facilitate downstream filtering of features
=cut
sub convert {
my $self = shift;
my @ann = @{$self->{anns}} if defined $self->{anns};;
my @seq = @{$self->{seqs}};
# not used yet
my @comp;
if ( $self->{comps} ) {
@comp = @{$self->{comps}}
}
# process the sequence elements
for ( @seq ) {
$self->_add_seq( $_ );
}
# process the annotation elements
for ( @ann ) {
$self->_annotation( $_ );
}
return $self->_order_feats( $self->{seq_h} );
}
=head2 _order_feats
Title : _order_feats
Usage : $self->_order_feats( $self->{seq_h} )
Function: an internal method to ensure the source feature comes first
and keep gene, mRNA and CDS features together
Returns : a ref. to an array containing the sequence object and a ref. to a list of features
Args : a ref. to a hash of sequences
=cut
sub _order_feats {
my ($self, $seqs) = @_;
my $seq = $self->{main_seq};
my $id = $seq->id;
my $ann = $self->{ann_l};
# make sure source(s) come first
my @src = grep { $_->primary_tag =~ /source|origin|\bregion\b/ } @$ann;
# preserve gene->mRNA->CDS or ncRNA->gene->transcript order
my @genes = grep { $_->primary_tag =~ /gene|CDS|[a-z]+RNA|transcript/ } @$ann;
my @other = sort { $a->start <=> $b->start || $b->end <=> $a->end }
grep { $_->primary_tag !~ /source|origin|\bregion\b/ }
grep { $_->primary_tag !~ /gene|mRNA|CDS/ } @$ann;
return [$seq, [@src, @genes, @other]];
}
=head2 _add_seq
Title : _add_seq
Usage : $self->_add_seq($seq_element)
Function: an internal method to process the sequence elements
Returns : nothing
Args : a sequence element
=cut
sub _add_seq {
my ($self, $el) = @_;
my $residues = '';
if ($el->{_residues}) {
$residues = $el->{_residues}->{Characters};
$residues =~ s/[ \n\r]//g;
$residues =~ s/\!//g;
$residues =~ tr/a-z/A-Z/;
}
else {
return 0;
}
my $id = $el->{Attributes}->{id};
my $ver = $el->{Attributes}->{version};
my $name = $el->{_name}->{Characters};
if ($name && $name ne $id) {
$self->complain("The sequence name and unique ID do not match. Using ID");
}
# get/set the sequence object
my $seq = $self->_seq($id);
# get/set the feature handler
my $featHandler = $self->_feat_handler;
# populate the sequence object
$seq->seq($residues);
$seq->seq_version($ver) if $ver;
# assume the id is the accession number
if ( $id =~ /^\w+$/ ) {
$seq->accession($id);
}
# If the focus attribute is set to "true", this is the main
# sequence
my $focus = 0;
if ( defined $el->{Attributes}->{focus} ) {
$self->{main_seq} = $seq;
$focus++;
}
# make sure real and annotated lengths match
my $length = $el->{Attributes}->{'length'};
$length && $seq->length(int($length));
if ( $seq->seq && defined($length) && $seq->length != int($length) ) {
$self->complain("The specified sequence has length ", $seq->length(),
" but the length attribute= ", $length);
$seq->seq( undef );
$seq->length( int($length) );
}
# deal with top-level annotations
my $tags = {};
if ( $el->{Attributes}->{md5checksum} ) {
$tags->{md5checksum} = [$el->{Attributes}->{md5checksum}];
}
if ($el->{_dbxref}) {
$tags->{dbxref} ||= [];
push @{$tags->{dbxref}}, $self->dbxref( $el->{_dbxref} );
}
if ($el->{_description}) {
my $desc = $el->{_description}->{Characters};
$seq->description( $desc );
}
if ($el->{_organism}) {
my @organism = split /\s+/, $el->{_organism}->{Characters};
if (@organism < 2) {
$self->complain("Species name should have at least two words");
}
else {
my $species = Bio::Species->new( -classification => [reverse @organism] );
$seq->species($species);
}
}
if ( defined($seq->species) ) {
$tags->{organism} = [$seq->species->binomial];
}
# elsif ($seq eq $self->{main_seq}) {
# $self->warn("The source organism for this sequence was\n" .
# "not specified. I will guess Drosophila melanogaster.\n" .
# "Otherwise, add <organism>Genus species</organism>\n" .
# "to the main sequence element");
# my @class = qw/ Eukaryota Metazoa Arthropoda Insecta Pterygota
# Neoptera Endopterygota Diptera Brachycera
# Muscomorpha Ephydroidea Drosophilidae Drosophila melanogaster/;
# my $species = Bio::Species->new( -classification => [ reverse @class ],
# -common_name => 'fruit fly' );
# $seq->species( $species );
# }
# convert GAME to bioperl molecule types
my $alphabet = $el->{Attributes}->{type};
if ( $alphabet ) {
$alphabet =~ s/aa/protein/;
$alphabet =~ s/cdna/rna/;
$seq->alphabet($alphabet);
}
# add a source feature if req'd
if ( !$self->{has_source} && $focus ) {
#$self->{source} = $featHandler->add_source($seq->length, $tags);
}
if ( $focus ) {
# add the map position
$self->_map_position( $self->{map_pos}, $seq );
$featHandler->{offset} = $self->{offset};
}
# prune the sequence from the parse tree
$self->flush;
}
=head2 _map_position
Title : _map_position
Usage : $self->_map_position($map_posn_element)
Function: an internal method to process the <map_position> element
Returns : nothing
Args : a map_position element
=cut
sub _map_position {
my ($self, $el) = @_;
# we can live without it
if ( !$el ) {
$self->{offset}= 0;
return 0;
}
# chromosome and coordinates
my $arm = $el->{_arm}->{Characters};
my $type = $el->{Attributes}->{type};
my $loc = $el->{_span};
my $start = $loc->{_start}->{Characters};
my $end = $loc->{_end}->{Characters};
# define the offset (may be a partial sequence)
# The coordinates will be relative but the CDS description
# coordinates may be absolute if the game-XML comes from apollo
# or gadfly
$self->{offset} = $start - 1;
my $seq_id = $el->{Attributes}->{seq};
my $seq = $self->{seq_h}->{$seq_id};
unless ( $seq ) {
$self->throw("Map position with no corresponding sequence object");
}
unless ($seq eq $self->{main_seq}){
$self->throw("Map position does not correspond to the main sequence");
}
my $species = '';
# create/update the top-level sequence feature if req'd
if ( $self->{source} ) {
my $feat = $self->{source};
unless ($feat->has_tag('organism')) {
$species = eval {$seq->species->binomial} || 'unknown species';
$feat->add_tag_value( organism => $species );
}
my %tags = ( mol_type => "genomic dna",
chromosome => $arm,
location => "$start..$end",
type => $type
);
for (keys %tags) {
$feat->add_tag_value( $_ => $tags{$_} );
}
$seq->add_SeqFeature($feat);
}
# come up with a description if there is none
my $desc = $seq->description;
if ( $species && $arm && $start && $end && !$desc) {
$seq->description("$species chromosome $arm $start..$end " .
"segment of complete sequence");
}
$self->flush;
}
=head2 _annotation
Title : _annotation
Usage : $self->_annotation($annotation_element)
Function: an internal method to process <annotation> elements
Returns : nothing
Args : an annotation element
=cut
sub _annotation {
my ($self, $el) = @_;
my $id = $el->{Attributes}->{id};
my $type = $el->{_type}->{Characters};
my $tags = {};
my $gname = $el->{_name}->{Characters} eq $id ? '' : $el->{_name}->{Characters};
# 'transposable element' is too long (breaks Bio::SeqIO::GenBank)
# $type =~ s/transposable_element/repeat_region/;
# annotations must be on the main sequence
my $seqid = $self->{main_seq}->id;
my $featHandler = $self->_feat_handler;
my @feats = ();
for my $child ( @{$el->{Children}} ) {
my $name = $child->{Name};
# these elements require special handling
if ( $name eq 'dbxref' ) {
$tags->{dbxref} ||= [];
push @{$tags->{dbxref}}, $self->dbxref( $child );
}
elsif ( $name eq 'aspect' ) {
$tags->{dbxref} ||= [];
push @{$tags->{dbxref}}, $self->dbxref( $child->{_dbxref} );
}
elsif ( $name eq 'feature_set' ) {
push @feats, $featHandler->feature_set( $id, $gname, $child, $type );
}
elsif ( $name eq 'comment' ) {
$tags->{comment} = [$self->comment( $child )];
}
elsif ( $name eq 'property' ) {
$self->property( $child, $tags );
}
elsif ( $name eq 'gene' ) {
# we may be dealing with an annotation that is not
# a gene, so we have to nest the gene inside it
$featHandler->has_gene( $child, $gname, $id )
}
# otherwise, tag/value pairs
# -- mild dtd enforcement
# synonym is not in the dtd but shows up in gadfly
# annotations
elsif ( $name =~ /type|synonym/ ) {
$tags->{$name} = [$child->{Characters}];
}
elsif ( $name ne 'name' ) {
$self->complain("Unrecognized element '$name'. I don't " .
"know what to do with $name elements in " .
"top-level sequence annotations." );
}
}
# add a gene annotation if required
unless ( $featHandler->has_gene || $type ne 'gene' ) {
$featHandler->has_gene( $el, $gname, $id )
}
if ( $tags->{symbol} ) {
if ( !$tags->{gene} ) {
$tags->{gene} = $tags->{symbol};
}
delete $tags->{symbol};
}
$featHandler->add_annotation( $self->{main_seq}, $type, $id, $tags, \@feats );
$self->flush;
}
# get/set the sequence object
=head2 _seq
Title : _seq
Usage : my $seq = $self->_seq
Function: an internal sequence getter/setter
Returns : a Bio::RichSeq object
Args : a sequence ID
=cut
sub _seq {
my ($self, $id) = @_;
$id || $self->throw("A unique id must be provided for the sequence");
my $seq = {};
if ( defined $self->{seq_h}->{$id}) {
$seq = $self->{seq_h}->{$id};
} else {
$seq = Bio::Seq::RichSeq->new( -id => $id );
$self->{seq_h}->{$id} = $seq; # store it
}
return $seq;
}
#get/set the feature handler
=head2 _feat_handler
Title : _feat_handler
Usage : my $featHandler = $self->_featHandler
Function: an internal getter/setter for feature handling objects
Returns : a Bio::SeqIO::game::featHandler object
Args : none
=cut
sub _feat_handler {
my $self = shift;
my $handler = {};
my $seq = $self->{main_seq};
if ( defined $self->{feat_handler} ) {
$handler = $self->{feat_handler};
}
else {
my @args = ( $seq, $self->{seq_h}, $self->{ann_l} );
$handler = Bio::SeqIO::game::featHandler->new( @args );
$self->{feat_handler} = $handler;
}
return $handler;
}
1;