view release on metacpan or  search on metacpan

Bio/Assembly/IO/maq.pm  view on Meta::CPAN

   my $readobj = Bio::LocatableSeq->new(
       -display_id => $$readinfo{'read_name'},
       -primary_id => $$readinfo{'read_name'},
       -seq        => $$readinfo{'seqstr'},
       -start      => 1,
       -strand     => $$readinfo{'strand'},
       -alphabet   => 'dna'
   );

   # Add read location and sequence to contig (in 'gapped consensus' coordinates)
   $$readinfo{'aln_start'} = $$readinfo{'posn'};
   $$readinfo{'aln_end'}   = $$readinfo{'posn'} + length($$readinfo{'seqstr'})-1;

   my $alncoord = Bio::SeqFeature::Generic->new(
       -primary     => $readobj->id,
       -start       => $$readinfo{'aln_start'},
       -end         => $$readinfo{'aln_end'},
       -strand      => $$readinfo{'strand'},
       -qual        => join(' ', $$readinfo{seq}->qual),
       # check here, need to create contigs "by hand"...
       -tag         => { 'contig' => $contigobj->id() }
   );

   $contigobj->set_seq_coord($alncoord, $readobj);

   # Add other misc read information as subsequence feature
   my @other = grep !/aln_(?:end|start)|seq(?:str)?|strand/, keys %$readinfo;
   my %other;
   @other{@other} = @$readinfo{@other};
   my $readtags = Bio::SeqFeature::Generic->new(
       -primary     => '_main_read_feature',
       -source      => $readobj->id,
       -start       => $$readinfo{'aln_start'},
       -end         => $$readinfo{'aln_end'},
       -strand      => $$readinfo{'strand'},
       # dumping ground:
       -tag         => \%other
   );
   $contigobj->get_features_collection->add_features([$readtags]);
   $contigobj->get_features_collection->add_SeqFeature($alncoord, $readtags);

   return $readobj;
}

#### revamp for maq

=head2 _store_singlet()

    Title   : _store_singlet
    Usage   : my $singletobj = $self->_store_read(\%readinfo, \%contiginfo);
    Function: store information of a singlet belonging to a scaffold in a singlet object
    Returns : Bio::Assembly::Singlet
    Args    : hash, hash

=cut

sub _store_singlet {
    my ($self, $contiginfo, $contigobj) = @_;

    my $contigid = $$contiginfo{'asmbl_id'};
    my $seqref = ($contigobj->each_seq())[0];
    my $singletobj = Bio::Assembly::Singlet->new( -id     => $contigid,
                                                  -seqref => $seqref   );

    # Add other misc contig information as features of the contig
    # Add other misc read information as subsequence feature
    #my @other = grep !/_sfc|_assembly|_elem/, keys %$contiginfo; # remove the objects; _elem contains a code ref and can't be frozen. Just shooting blind here.
    #my %other;
    #@other{@other} = @$contiginfo{@other};
    #my $contigtags = Bio::SeqFeature::Generic->new(
    #    -primary     => '_main_contig_feature',
    #    -source      => $$contiginfo{asmbl_id},
    #    -start       => 1,
    #    -end         => $singletobj->get_consensus_length(),
    #    -strand      => 1,
    #    # dumping ground:
    #    -tag         => \%other
    #);
    #$singletobj->add_features([ $contigtags ], 1);

    #$$readinfo{'aln_start'} = $$readinfo{'start'};
    #$$readinfo{'aln_end'} = $$readinfo{'end'};
    #$$readinfo{'strand'} = ($$readinfo{strand} eq '+' ? 1 : -1);
    #my $alncoord = Bio::SeqFeature::Generic->new(
    #    -primary     => '_aligned_coord',
    #    -source      => $$readinfo{read_name},
    #    -start       => $$readinfo{'start'},
    #    -end         => $$readinfo{'end'},
    #    -strand      => $$readinfo{'strand'},
    #    -tag         => { 'contig' => $$contiginfo{asmbl_id} }
    #    );
    #$alncoord->attach_seq($singletobj->seqref);
    #$singletobj->add_features([ $alncoord ], 0);

    # Add other misc read information as subsequence feature
    #my @other = grep !/seqstr|strand/, keys %$readinfo;
    #my %other;
    #@other{@other} = @$readinfo{@other};
    #my $readtags = Bio::SeqFeature::Generic->new(
    #    -primary     => '_main_read_feature',
    #    -source      => $$readinfo{read_name},
    #    -start       => $$readinfo{'aln_start'},
    #    -end         => $$readinfo{'aln_end'},
    #    -strand      => $$readinfo{'strand'},
    #    # dumping ground:
    #    -tag         => \%other
    #    );
    #$singletobj->get_features_collection->add_features([$readtags]);
    #$singletobj->get_features_collection->add_SeqFeature($alncoord, $readtags);

    return $singletobj;
}

###### writes -- need them??

=head2 write_assembly()

    Title   : write_assembly
    Usage   : 
    Function: not currently available for maq assemblies
    Returns : throw
    Args    :