Bio::AlignIO
bl2seq
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Summary
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
Package variables
No package variables defined.
Included modules
Inherit
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 : 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 _initialize
{ my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
my ($rt) = $self->_rearrange([qw(REPORT_TYPE)],@args);
defined $rt && $self->report_type($rt);} | 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;
}
if (!defined $self->{'_hit'}) {
delete $self->{'_result'};
next;
}
my $hsp = $self->{'_hit'}->next_hsp;
if (!defined $hsp) {
delete $self->{'_hit'};
next;
}
$hsp ? return $hsp->get_aln: return;
}} | sub write_aln
{ my ($self,@aln) = @_;
$self->throw_not_implemented();} | sub report_type
{ my $self = shift;
return $self->{'report_type'} = shift if @_;
return $self->{'report_type'};
}
1;} | 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://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
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 Schattner | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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)