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# $Id: StandAloneWUBlast.pm 15383 2009-01-16 16:45:08Z cjfields $
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# BioPerl module for Bio::Tools::Run::StandAloneBlast
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# Copyright Peter Schattner
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::Tools::Run::StandAloneWUBlast - Object for the local execution
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# Do not use directly; use Bio::Tools::Run::StandAloneBlast
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See Bio::Tools::Run::StandAloneBlast
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via
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http://bugzilla.open-bio.org/
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=head1 AUTHOR - Peter Schattner
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Email schattner at alum.mit.edu
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=head1 MAINTAINER - Torsten Seemann
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Email torsten at infotech.monash.edu.au
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Sendu Bala bix@sendu.me.uk (reimplementation)
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The rest of the documentation details each of the object
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methods. Internal methods are usually preceded with a _
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package Bio::Tools::Run::StandAloneWUBlast;
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use base qw(Bio::Tools::Run::StandAloneBlast);
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our $DEFAULTREADMETHOD = 'BLAST';
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# If local BLAST databases are not stored in the standard
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# /data directory, the variable BLASTDATADIR will need to be
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our $DATADIR = $Bio::Tools::Run::StandAloneBlast::DATADIR;
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our %GENERAL_PARAMS = (i => 'input',
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our @WUBLAST_PARAMS = qw(e s e2 s2 w t x m y z l k h v b q r
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matrix filter wordmask filter maskextra hitdist wink ctxfactor gape
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gaps gape2 gaps2 gapw gapx olf golf olmax golmax gapdecayrate
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topcombon topcomboe sumstatsmethod hspsepqmax hspsepsmax gapsepqmax
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gapsepsmax altscore hspmax gspmax qoffset nwstart nwlen qrecmin qrecmax
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dbrecmin dbrecmax vdbdescmax dbchunks sort_by_pvalue cpus putenv
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our @WUBLAST_SWITCH = qw(kap sump poissonp lcfilter lcmask echofilter
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stats nogap gapall pingpong nosegs postsw span2 span1 span prune
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consistency links ucdb gi noseqs qtype qres sort_by_pvalue
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sort_by_count sort_by_highscore sort_by_totalscore
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sort_by_subjectlength mmio nonnegok novalidctxok shortqueryok notes
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warnings errors endputenv getenv endgetenv abortonerror abortonfatal);
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our @OTHER_PARAMS = qw(_READMETHOD);
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Usage : my $obj = Bio::Tools::Run::StandAloneBlast->new();
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Function: Builds a newBio::Tools::Run::StandAloneBlast object
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Returns : Bio::Tools::Run::StandAloneBlast
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Args : -quiet => boolean # make program execution quiet
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-_READMETHOD => 'BLAST' (default, synonym 'SearchIO') || 'blast_pull'
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# the parsing method, case insensitive
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Essentially all BLAST parameters can be set via StandAloneBlast.pm.
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Some of the most commonly used parameters are listed below. All
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parameters have defaults and are optional except for -p.
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-p Program Name [String]
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Input should be one of "wublastp", "wublastn", "wublastx",
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"wutblastn", or "wutblastx".
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-d Database [String] default = nr
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The database specified must first be formatted with xdformat.
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-E Expectation value (E) [Real] default = 10.0
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-o BLAST report Output File [File Out] Optional,
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default = ./blastreport.out ; set by StandAloneBlast.pm
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my ($caller, @args) = @_;
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my $self = $caller->SUPER::new(@args);
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$self->_set_from_args(\@args, -methods => {(map { $_ => $GENERAL_PARAMS{$_} } keys %GENERAL_PARAMS),
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(map { $_ => $_ } (@OTHER_PARAMS,
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my ($tfh, $tempfile) = $self->io->tempfile();
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my $outfile = $self->o || $self->outfile || $tempfile;
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$self->_READMETHOD($DEFAULTREADMETHOD) unless $self->_READMETHOD;
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# We let get/setter method names be case-insensitve
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my $attr = $AUTOLOAD;
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$self->can($attr) || $self->throw("Unallowed parameter: $orig !");
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return $self->$attr(@_);
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Usage : $blast_report = $factory->wublast('t/testquery.fa');
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$input = Bio::Seq->new(-id=>"test query",
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-seq=>"ACTACCCTTTAAATCAGTGGGGG");
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$blast_report = $factory->wublast($input);
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$seq_array_ref = \@seq_array; # where @seq_array is an array of Bio::Seq objects
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$blast_report = $factory->wublast(\@seq_array);
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Returns : Reference to a Blast object
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Args : Name of a file or Bio::Seq object or an array of
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Bio::Seq object containing the query sequence(s).
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Throws an exception if argument is not either a string
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(eg a filename) or a reference to a Bio::Seq object
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(or to an array of Seq objects). If argument is string,
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throws exception if file corresponding to string name can
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my ($self, $input1) = @_;
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$self->io->_io_cleanup();
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my $executable = 'wublast';
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# Create input file pointer
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my $infilename1 = $self->_setinput($executable, $input1) || $self->throw("$input1 not Bio::Seq object or array of Bio::Seq objects or file name!");
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$self->i($infilename1);
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my $blast_report = $self->_generic_local_wublast($executable);
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=head2 _generic_local_wublast
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Title : _generic_local_wublast
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Usage : internal function not called directly
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Returns : Blast object
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Args : Reference to calling object and name of BLAST executable
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sub _generic_local_wublast {
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my $executable = shift;
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# Create parameter string to pass to Blast program
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my $param_string = $self->_setparams($executable);
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$param_string = " ".$self->database." ".$self->input." ".$param_string;
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my $blast_report = $self->_runwublast($executable, $param_string);
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Usage : Internal function, not to be called directly
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Function: makes actual system call to WU-Blast program
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Returns : Report Blast object
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Args : Reference to calling object, name of BLAST executable,
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and parameter string for executable
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my ($self, $executable, $param_string) = @_;
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my ($blast_obj, $exe);
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if (! ($exe = $self->executable($self->p))){
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$self->warn("cannot find path to $executable");
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my $commandstring = $exe.$param_string;
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$self->debug("$commandstring\n");
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system($commandstring) && $self->throw("$executable call crashed: $? | $! | $commandstring\n");
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my $outfile = $self->o();
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$blast_obj = Bio::SearchIO->new(-file => $outfile, -format => 'blast');
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Usage : Internal function, not to be called directly
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Function: Create parameter inputs for Blast program
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Returns : parameter string to be passed to Blast
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Args : Reference to calling object and name of BLAST executable
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my ($self, $executable) = @_;
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my ($attr, $value, @execparams);
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@execparams = @WUBLAST_PARAMS;
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# of the general params, wublast only takes outfile at
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# this stage (we add in program, input and database manually elsewhere)
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push(@execparams, 'o');
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# workaround for problems with shell metacharacters [bug 2707]
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# simply quoting does not always work!
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# Fixed so Windows files are not quotemeta'd
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$self->o(quotemeta($tmp)) if ($tmp && $^O !~ /^MSWin/);
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my $param_string = $self->SUPER::_setparams(-params => [@execparams],
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-switches => \@WUBLAST_SWITCH,
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$self->o($tmp) if ($tmp && $^O !~ /^MSWin/);
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if ($self->quiet()) {
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$param_string .= ' 2> '.File::Spec->devnull;
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return $param_string;
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Bio/Tools/Run/StandAloneWUBlast.pm
