Bio::SeqIO::game seqHandler
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqIO::game::seqHandler -- a class for handling game-XML sequences
Package variables
No package variables defined.
Included modules
Bio::Seq::RichSeq
Bio::SeqFeature::Generic
Bio::SeqIO::game::featHandler
Bio::Species
Data::Dumper
strict
Inherit
Bio::SeqIO::game::gameSubs
Synopsis
This modules is not used directly
Description
Bio::SeqIO::game::seqHandler processes all of the sequences associated with a game record
and, via feature handlers, processes the associated annotations
Methods
newDescriptionCode
convertDescriptionCode
_order_featsDescriptionCode
_add_seqDescriptionCode
_map_positionDescriptionCode
_annotationDescriptionCode
_seqDescriptionCode
_feat_handlerDescriptionCode
Methods description
newcode    nextTop
 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
convertcodeprevnextTop
 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
_order_featscodeprevnextTop
 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
_add_seqcodeprevnextTop
 Title   : _add_seq
Usage : $self->_add_seq($seq_element)
Function: an internal method to process the sequence elements
Returns : nothing
Args : a sequence element
_map_positioncodeprevnextTop
 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
_annotationcodeprevnextTop
 Title   : _annotation
Usage : $self->_annotation($annotation_element)
Function: an internal method to process <annotation> elements
Returns : nothing
Args : an annotation element
_seqcodeprevnextTop
 Title   : _seq
Usage : my $seq = $self->_seq
Function: an internal sequence getter/setter
Returns : a Bio::RichSeq object
Args : a sequence ID
_feat_handlercodeprevnextTop
 Title   : _feat_handler
Usage : my $featHandler = $self->_featHandler
Function: an internal getter/setter for feature handling objects
Returns : a Bio::SeqIO::game::featHandler object
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($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;
}
convertdescriptionprevnextTop
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( $self->{seq_h} );
}
_order_featsdescriptionprevnextTop
sub _order_feats {
    my ($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 [$seq, [@src, @genes, @other]];
}
_add_seqdescriptionprevnextTop
sub _add_seq {
    my ($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
$self->flush;
}
_map_positiondescriptionprevnextTop
sub _map_position {
    my ($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"); } $self->flush;
}
_annotationdescriptionprevnextTop
sub _annotation {
    my ($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 ); $self->flush; } # get/set the sequence object
}
_seqdescriptionprevnextTop
sub _seq {
    my ($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
}
_feat_handlerdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Sheldon McKayTop
Email mckays@cshl.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _