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.IX Title "Bio::Tools::Run::StandAloneBlastPlus::BlastMethods 3pm"
.TH Bio::Tools::Run::StandAloneBlastPlus::BlastMethods 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods \- Provides BLAST methods to StandAloneBlastPlus
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\& # create a factory:
\& $fac = Bio::Tools::Run::StandAloneBlastPlus\->new(
\&    \-db_name => \*(Aqtestdb\*(Aq
\& );
\& # get your results
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq,
\&                         \-outfile => \*(Aqquery.bls\*(Aq,
\&                         \-method_args => [ \*(Aq\-num_alignments\*(Aq => 10 ] );
\&
\& $result = $fac\->tblastx( \-query => $an_alignment_object,
\&                          \-outfile => \*(Aqquery.bls\*(Aq,
\&                          \-outformat => 7 );
\& # do a bl2seq
\& $fac\->bl2seq( \-method => \*(Aqblastp\*(Aq,
\&               \-query => $seq_object_1,
\&               \-subject => $seq_object_2 );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module provides the \s-1BLAST\s0 methods (blastn, blastp, psiblast,
etc.) to the Bio::Tools::Run::StandAloneBlastPlus object.
.SH "USAGE"
.IX Header "USAGE"
This \s-1POD\s0 describes the use of \s-1BLAST\s0 methods against a
Bio::Tools::Run::StandAloneBlastPlus factory object. The object
itself has extensive facilities for creating, formatting, and masking
\&\s-1BLAST\s0 databases; please refer to
Bio::Tools::Run::StandAloneBlastPlus \s-1POD\s0 for these details.
.PP
Given a \f(CW\*(C`StandAloneBlastPlus\*(C'\fR factory, such as
.PP
.Vb 3
\& $fac = Bio::Tools::Run::StandAloneBlastPlus\->new(
\&    \-db_name => \*(Aqtestdb\*(Aq
\& );
.Ve
.PP
you can run the desired \s-1BLAST\s0 method directly from the factory object,
against the database currently attached to the factory (in the
example, \f(CW\*(C`testdb\*(C'\fR). \f(CW\*(C`\-query\*(C'\fR is a required argument:
.PP
.Vb 1
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq );
.Ve
.PP
Here, \f(CW$result\fR is a Bio::Search::Result::BlastResult object.
.PP
Other details:
.IP "\(bu" 4
The blast output file can be named explicitly:
.Sp
.Vb 2
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq,
\&                         \-outfile => \*(Aqquery.bls\*(Aq );
.Ve
.IP "\(bu" 4
The output format can be specified:
.Sp
.Vb 3
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq,
\&                         \-outfile => \*(Aqquery.bls\*(Aq,
\&                         \-outformat => 7 ); #tabular
.Ve
.IP "\(bu" 4
Additional arguments to the method can be specified:
.Sp
.Vb 4
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq,
\&                         \-outfile => \*(Aqquery.bls\*(Aq,
\&                         \-method_args => [ \*(Aq\-num_alignments\*(Aq => 10 ,
\&                                           \*(Aq\-evalue\*(Aq => 100 ]);
.Ve
.IP "\(bu" 4
\&\s-1HTML\s0 output can be created using this workaround:
.Sp
.Vb 3
\& $result = $fac\->blastn( \-query => \*(Aqquery_seqs.fas\*(Aq,
\&                         \-outfile => \*(Aqquery.bls\*(Aq,
\&                         \-method_args => [ \-html => \*(Aq \*(Aq );
.Ve
.IP "\(bu" 4
To get the name of the blast output file, do
.Sp
.Vb 1
\& $file = $fac\->blast_out;
.Ve
.IP "\(bu" 4
To clean up the temp files (you must do this explicitly):
.Sp
.Vb 1
\& $fac\->cleanup;
.Ve
.SS "\fBbl2seq()\fP"
.IX Subsection "bl2seq()"
Running \f(CW\*(C`bl2seq\*(C'\fR is similar, but both \f(CW\*(C`\-query\*(C'\fR and \f(CW\*(C`\-subject\*(C'\fR are
required, and the attached database is ignored. The blast method must
be specified explicitly with the \f(CW\*(C`\-method\*(C'\fR parameter:
.PP
.Vb 3
\& $fac\->bl2seq( \-method => \*(Aqblastp\*(Aq,
\&               \-query => $seq_object_1,
\&               \-subject => $seq_object_2 );
.Ve
.PP
Other parameters ( \f(CW\*(C`\-method_args\*(C'\fR, \f(CW\*(C`\-outfile\*(C'\fR, and \f(CW\*(C`\-outformat\*(C'\fR ) are valid.
.SS "Return values"
.IX Subsection "Return values"
The return value is always a Bio::Search::Result::BlastResult
object on success, undef on failure.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Tools::Run::StandAloneBlastPlus, Bio::Tools::Run::BlastPlus
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
Email maj \-at\- fortinbras \-dot\- us
.PP
Describe contact details here
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "\fBrun()\fP"
.IX Subsection "run()"
.Vb 10
\& Title   : run
\& Usage   :
\& Function: Query the attached database using a specified blast
\&           method
\& Returns : Bio::Search::Result::BlastResult object
\& Args    : key => value:
\&           \-method => $method [blastp|blastn|blastx|tblastx|tblastn|
\&                               rpsblast|psiblast|rpstblastn]
\&           \-query => $query_sequences (a fasta file name or BioPerl sequence
\&                      object or sequence collection object)
\&           \-outfile => $blast_report_file (optional: default creates a tempfile)
\&           \-outformat => $format_code (integer in [0..10], see blast+ docs)
\&           \-method_args => [ \-key1 => $value1, ... ] (additional arguments
\&                         for the given method)
.Ve
.SS "\fBbl2seq()\fP"
.IX Subsection "bl2seq()"
.Vb 12
\& Title   : bl2seq
\& Usage   :
\& Function: emulate bl2seq using blast+ programs
\& Returns : Bio::Search::Result::BlastResult object
\& Args    : key => value
\&           \-method => $blast_method [blastn|blastp|blastx|
\&                                     tblastn|tblastx]
\&           \-query => $query (fasta file or BioPerl sequence object
\&           \-subject => $subject (fasta file or BioPerl sequence object)
\&           \-outfile => $blast_report_file
\&           \-method_args => [ $key1 => $value1, ... ] (additional method
\&                        parameters)
.Ve
.SS "\fBnext_result()\fP"
.IX Subsection "next_result()"
.Vb 5
\& Title   : next_result
\& Usage   : $result = $fac\->next_result;
\& Function: get the next BLAST result
\& Returns : Bio::Search::Result::BlastResult object
\& Args    : none
.Ve
.SS "\fBrewind_results()\fP"
.IX Subsection "rewind_results()"
.Vb 5
\& Title   : rewind_results
\& Usage   : $fac\->rewind_results;
\& Function: rewind BLAST results
\& Returns : true on success
\& Args    :
.Ve
.SS "\fBblast_out()\fP"
.IX Subsection "blast_out()"
.Vb 5
\& Title   : blast_out
\& Usage   : $file = $fac\->blast_out
\& Function: get the filename of the blast report file
\& Returns : scalar string
\& Args    : none
.Ve