Summary

Bio::SeqIO::chado - chado sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

It is probably best not to use this object directly, but
rather go through the SeqIO handler system. Go:

    $stream = Bio::SeqIO->new(-file => $filename, -format => 'chado');

    while ( my $seq = $stream->next_seq() ) {
	# do something with $seq
    }

Description

This object can transform Bio::Seq objects to and from chado flat
file databases. CURRENTLY ONLY TO    (output only) shows the dna or not
   (output only) provides a sorting func which is applied to the FTHelpers
before printing

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq

Methods code

sub _initialize {

    my($self,@args) = @_;
    
    $self->SUPER::_initialize(@args); 
    if( ! defined $self->sequence_factory ) {
	$self->sequence_factory(new Bio::Seq::SeqFactory
				(-verbose => $self->verbose(), 
				 -type => 'Bio::Seq::RichSeq'));
    }
    my $wclass = $self->default_handler_class;
    $self->handler($wclass->new);
    $self->{_end_of_data} = 0;
    $self->handler->S("chado");
    return;

}

sub DESTROY {

    my $self = shift;
    $self->end_of_data();
    $self->SUPER::DESTROY();

}

sub end_of_data {

    my $self = shift;
    $self->{_end_of_data} = 1;
    $self->handler->E("chado");

}

sub default_handler_class {

    return "Data::Stag::BaseHandler";

}

sub next_seq {

    my ($self,@args) = @_;
    my $seq = $self->sequence_factory->create
	(
         #         '-verbose' =>$self->verbose(), 
         #	 %params,
         #	 -seq => $seqc,
         #	 -annotation => $annotation,
         #	 -features => \@features
        );
    return $seq;

}

sub handler {

    my $self = shift;
    $self->{_handler} = shift if @_;
    return $self->{_handler};

}

sub write_seq {

    my ($self,$seq) = @_;
    
    if( !defined $seq ) {
	$self->throw("Attempting to write with no seq!");
    }
    
    if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
	$self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
    }

    # get a handler - must inherit from Data::Stag::BaseHandler;
    my $w = $self->handler;

    # start of data
    $w->S("seqset");

    #    my $seq_temp_uid = $self->get_temp_uid($seq);

    my $seq_temp_uid = $seq->accession . '.' . ($seq->can('seq_version') ? $seq->seq_version : $seq->version);

    # data structure representing the core sequence for this record
    my $seqnode =
      Data::Stag->new(feature=>[
                                    [feature_id=>$seq_temp_uid],
                                    [dbxrefstr=>$seq->accession_number],
                                    [name=>$seq->display_name],
                                    [residues=>$seq->seq],
                                   ]);
    
    # soft properties
    my %prop = ();

    my ($div, $mol);
    my $len = $seq->length();

    if ( $seq->can('division') ) {
	$div=$seq->division;
    } 
    if( !defined $div || ! $div ) { $div = 'UNK'; }

    if( !$seq->can('molecule') || ! defined ($mol = $seq->molecule()) ) {
	$mol = $seq->alphabet || 'DNA';
    }
    
    
    my $circular = 'linear  ';
    $circular = 'circular' if $seq->is_circular;

    # cheeky hack - access symbol table
    no strict 'refs';
    map {
        $prop{$_} = 
          $ {*$_};
    } qw(mol div circular);
    use strict 'refs';

    map {
        $prop{$_} = $seq->$_() if $seq->can($_);
    } qw(desc keywords);

    local($^W) = 0;   # supressing warnings about uninitialized fields.
    
    # Organism lines
    if (my $spec = $seq->species) {
        my ($species, $genus, @class) = $spec->classification();
	my $OS;
        if( $spec->common_name ) {
	    $OS = $spec->common_name;
	} else { 
	    $OS = "$genus $species";
	}
        if (my $ssp = $spec->sub_species) {
            $OS .= " $ssp";
        }
    }
    
    # Reference lines
    my $count = 1;
    foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
        # TODO
    }
    # Comment lines
    
    foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
        $seqnode->add_featureprop([[pkey=>'comment'],[pval=>$comment->text]]);
    }

    # throw the writer an event
    $w->ev(@$seqnode);

    $seqnode = undef;      # free memory

    # make events for all the features within the record
    foreach my $sf ( $seq->top_SeqFeatures ) {
        $self->write_sf($sf, $seq_temp_uid);
    }

    # data end
    $w->E("seqset");
    return 1;

}

sub write_sf {

    my $self = shift;
    my $sf = shift;
    my $seq_temp_uid = shift;

    my $w = $self->handler;

    my %props =
      map {
          $_=>[$sf->each_tag_value($_)]
      } $sf->all_tags;

    my $loc = $sf->location;
    my $name = $sf->display_name;
    my $type = $sf->primary_tag;
    my @subsfs = $sf->sub_SeqFeature;
    my @locnodes = ();
    my $sid = $loc->is_remote ? $loc->seq_id : $seq_temp_uid;
    if( $loc->isa("Bio::Location::SplitLocationI") ) {
        # turn splitlocs into subfeatures
        my $n = 1;
        push(@subsfs,
             map {
                 my $ssf =
                   Bio::SeqFeature::Generic->new(

                                                 -start=>$_->start,
                                                 -end=>$_->end,
                                                 -strand=>$_->strand,
                                                 -primary=>$self->subpartof($type),
                                              );
                 if ($_->is_remote) {
                     $ssf->location->is_remote(1);
                     $ssf->location->seq_id($_->seq_id);
                 }
                 $ssf;
               } $loc->each_Location);
    }
    elsif( $loc->isa("Bio::Location::RemoteLocationI") ) {
        # turn splitlocs into subfeatures
        my $n = 1;
        push(@subsfs,
             map {
                 Bio::SeqFeature::Generic->new(
#                                               -name=>$name.'.'.$n++,
                                               -start=>$_->start,
                                               -end=>$_->end,
                                               -strand=>$_->strand,
                                               -primary=>$self->subpartof($type),
                                              )
               } $loc->each_Location);
    }
    else {
        my ($beg, $end, $strand) = $self->bp2ib($loc);
        @locnodes = (
                     [featureloc=>[
                                   [nbeg=>$beg],
                                   [nend=>$end],
                                   [strand=>$strand],
                                   [srcfeature_id=>$sid],
                                   [group=>0],
                                   [rank=>0],
                                  ]
                     ]
                    );
    }
    my $feature_id = $self->get_temp_uid($sf);
    
    my $fnode =
      [feature=>[
                 [feature_id=>$feature_id],
                 [name=>$name],
                 [typename=>$type],
                 @locnodes,
                 (map {
                     my $k = $_;
                     map { [featureprop=>[[pkey=>$k],[pval=>$_]]] } @{$props{$k}}
                 } keys %props),
                ]];
    $w->ev(@$fnode);

    foreach my $ssf (@subsfs) {
        my $ssfid = $self->write_sf($ssf, $sid);
        $w->ev(feature_relationship=>[
                                      [subjfeature_id=>$ssfid],
                                      [objfeature_id=>$feature_id]
                                     ]
              );
    }
    return $feature_id;

}

sub session_id {

    my $self = shift;
    $self->{_session_id} = shift if @_;
    if (!$self->{_session_id}) {
        $self->{_session_id} = $$.time;
    }
    return $self->{_session_id};

}

sub get_temp_uid {

    my $self = shift;
    my $ob = shift;
    my $id = $obj2id_hash{$ob};
    if (!$id) {
        $id = $next_id++;
        $obj2id_hash{$ob} = $id;
    }
    return $self->session_id.'.'.$id;

}

sub bp2ib {

    my $self = shift;
    my $loc = shift;
    my ($s, $e, $str) = 
      ref($loc) eq "ARRAY" ? (@$loc) : ($loc->start, $loc->end, $loc->strand);
    if ($str < 0) {
        ($s, $e) = ($e, $s);
    }
    $s--;
    return ($s, $e, $str);

}

sub subpartof {

    my $self = shift;
    my $type = 'partof_'.shift;
    $type =~ s/partof_CDS/CDS_exon/;
    $type =~ s/partof_\wRNA/exon/;
    return $type;

}

General documentation

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://www.bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

Email cjm@fruitfly.org

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _