Bio::AlignIO bl2seq
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::SearchIO
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');
    $aln = $in->next_aln();
Description
This object can create Bio::SimpleAlign sequence alignment objects (of
2 sequences) from bl2seq BLAST reports.
A nice feature of this module is that- in combination with
StandAloneBlast.pm or remote blasting - it can be used to align 2
sequences and make a SimpleAlign object from them which can then be
manipulated using any SimpleAlign.pm methods, eg:
   #Get 2 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);

   # 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
new
No description
Code
next_alnDescriptionCode
write_alnDescriptionCode
report_typeDescriptionCode
Methods description
next_alncode    nextTop
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : NONE
write_alncodeprevnextTop
 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
report_typecodeprevnextTop
 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
newdescriptionprevnextTop
sub new {
     my ($class) = shift;
    my $self = $class->SUPER::new(@_);
    my ($rt) = $self->_rearrange([qw(REPORT_TYPE)],@_);
    $self->report_type($rt);
    $self;
}
next_alndescriptionprevnextTop
sub next_aln {
    my $self = shift;
    my ($start,$end,$name,$seqname,$seq,$seqchar,$strand);
    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 $hsp->get_aln;
# much easier above, eh?
# $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 $aln;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;

    $self->throw("Sorry: writing bl2seq output is not available! /n");
}
report_typedescriptionprevnextTop
sub report_type {
    my $self = shift;
    return $self->{'report_type'} = shift if @_;
    return $self->{'report_type'};
}
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://bio.perl.org/MailList.html   - About the mailing lists
Reporting BugsTop
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://bugzilla.bioperl.org/
AUTHOR - Peter SchattnerTop
Email: schattner@alum.mit.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _