.\" -*- mode: troff; coding: utf-8 -*- .\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>. .ie n \{\ . ds C` "" . ds C' "" 'br\} .el\{\ . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Bio::Tools::Run::StandAloneBlastPlus::BlastMethods 3pm" .TH Bio::Tools::Run::StandAloneBlastPlus::BlastMethods 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .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 BLAST methods (blastn, blastp, psiblast, etc.) to the Bio::Tools::Run::StandAloneBlastPlus object. .SH USAGE .IX Header "USAGE" This POD describes the use of BLAST methods against a Bio::Tools::Run::StandAloneBlastPlus factory object. The object itself has extensive facilities for creating, formatting, and masking BLAST databases; please refer to Bio::Tools::Run::StandAloneBlastPlus POD 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 BLAST 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 HTML 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