Bio::AlignIO bl2seq
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Summary
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
Package variables
No package variables defined.
Included modules
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", -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
_initialize
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 on success,
undef on error or end of file
Args : none
write_aln (NOT IMPLEMENTED)codeprevnextTop
 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
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);
    my ($rt) = $self->_rearrange([qw(REPORT_TYPE)],@args);
    defined $rt && $self->report_type($rt);
}
next_alndescriptionprevnextTop
sub next_aln {
    my $self = shift;
    unless (exists $self->{'_searchio'}) {
        $self->{'_searchio'} = Bio::SearchIO->new(-fh => $self->_fh,
                   -format => 'blast',
                   -report_type => $self->report_type);
    }
    while (1) {
        if (!exists $self->{'_result'}) {
            $self->{'_result'} = $self->{'_searchio'}->next_result;
        }
        return if !defined $self->{'_result'};
        if (!exists $self->{'_hit'}) {
            $self->{'_hit'} = $self->{'_result'}->next_hit;
        }
        # out of hits for this result?
if (!defined $self->{'_hit'}) { delete $self->{'_result'}; next; } my $hsp = $self->{'_hit'}->next_hsp; # out of hsps for this hit?
if (!defined $hsp) { delete $self->{'_hit'}; next; } $hsp ? return $hsp->get_aln: return; }
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;
    $self->throw_not_implemented();
}
report_typedescriptionprevnextTop
sub report_type {
    my $self = shift;
    return $self->{'report_type'} = shift if @_;
    return $self->{'report_type'};
}

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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
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 _
newTop
 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)