Summary

Bio::AlignIO::bl2seq - bl2seq sequence input/output stream

Package variables

Included modules

Inherit

Bio::AlignIO

Synopsis

Do not use this module directly. Use it via the Bio::AlignIO class, as in:

    use Bio::AlignIO;

    $in  = Bio::AlignIO->new(-file   => "inputfilename" ,
                             -format => "bl2seq",
                             -report_type => "blastn");
    $aln = $in->next_aln();

Description

This object can create Bio::SimpleAlign sequence alignment objects (of
two sequences) from bl2seq BLAST reports.
A nice feature of this module is that - in combination with
Bio::Tools::Run::StandAloneBlast.pm or a remote BLAST - it can be used to
align two sequences and make a Bio::SimpleAlign object from them which
can then be manipulated using any Bio::SimpleAlign methods, eg:

   # Get two sequences
   $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
   my $seq3 = $str->next_seq();
   my $seq4 = $str->next_seq();

   # Run bl2seq on them
   $factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp',
                                               'outfile' => 'bl2seq.out');
   my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
   # Note that report is a Bio::SearchIO object

   # Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
   $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
   $aln = $str->next_aln();

Methods

Methods description

 Title   : new
 Usage   : my $alignio = Bio::SimpleAlign->new(-format => 'bl2seq',
                                               -file   => 'filename',
                                               -report_type => 'blastx');
 Function: Get a Bio::SimpleAlign
 Returns : Bio::SimpleAlign object
 Args    : -report_type => report type (blastn,blastx,tblastx,tblastn,blastp)

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object on success,
           undef on error or end of file
 Args    : none

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in bl2seq format
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

 Title   : report_type
 Usage   : $obj->report_type($newval)
 Function: Sets the report type (blastn, blastp...)
 Returns : value of report_type (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

Methods code

sub new {

    my ($class) = shift;
    my $self = $class->SUPER::new(@_);
    my ($rt) = $self->_rearrange([qw(REPORT_TYPE)],@_);
    defined $rt && $self->report_type($rt);
    return $self;

}

sub next_aln {

    my $self = shift;
    my $aln =  Bio::SimpleAlign->new(-source => 'bl2seq');
    $self->{'bl2seqobj'} = $self->{'bl2seqobj'} ||
	Bio::SearchIO->new(-fh => $self->_fh,
			   -format => 'blast');
    my $bl2seqobj = $self->{'bl2seqobj'};
    my $result = $self->{'_result'} || $bl2seqobj->next_result;
    $self->{'result'} = undef, return unless defined $result;

    my $hit = $self->{'_hit'} || $result->next_hit;
    $self->{'_hit'} = undef, return unless defined $hit;

    my $hsp  = $hit->next_hsp;
    return unless defined $hsp;
    return $hsp->get_aln;

# much easier above, eh?
#     my ($start,$end,$name,$seqname,$seq,$seqchar,$strand);
#     $seqchar = $hsp->query_string;
#     $start   = $hsp->query->start;
#     $end     = $hsp->query->end;
#      # Query name typically not present in bl2seq report
#     $seqname = $hsp->query->seq_id || 'Query-sequence';
#     $strand  = $hsp->query->strand;

#     #    unless ($seqchar && $start && $end  && $seqname) {return 0} ;
#     unless ($seqchar && $start && $end ) {return 0} ;

#     $seq = new Bio::LocatableSeq('-seq'   =>$seqchar,
# 				 '-id'    =>$seqname,
# 				 '-start' =>$start,
# 				 '-end'   =>$end,
# 				 '-strand'=>$strand,
# 				 );

#     $aln->add_seq($seq);

#     $seqchar  = $hsp->hit_string;
#     $start    = $hsp->hit->start;
#     $end      = $hsp->hit->end;
#     $seqname  = $hsp->hit->seq_id;
#     $strand   = $hsp->hit->strand;

#     unless ($seqchar && $start && $end  && $seqname) {return 0} ;

#     $seq = new Bio::LocatableSeq('-seq'   =>$seqchar,
# 				 '-id'    =>$seqname,
# 				 '-start' =>$start,
# 				 '-end'   =>$end,
# 				 '-strand'=>$strand,
# 				 );
#     $aln->add_seq($seq);
#     return $aln;

}

sub write_aln {

    my ($self,@aln) = @_;
    $self->throw_not_implemented();

}

sub report_type {

    my $self = shift;
    return $self->{'report_type'} = shift if @_;
    return $self->{'report_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
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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:

  http://bugzilla.open-bio.org/

Email: schattner@alum.mit.edu

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