| Bio::AlignIO::bl2seq(3pm) | User Contributed Perl Documentation | Bio::AlignIO::bl2seq(3pm) |
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
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();
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();
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://github.com/bioperl/bioperl-live/issues
Email: schattner@alum.mit.edu
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 L<Bio::SimpleAlign>
Returns : L<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 : L<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 : L<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)
| 2021-08-15 | perl v5.32.1 |