Bio::Tools::Run::StandUsereContributed PerlBio::Tools::Run::StandAloneBlast(3)NAMEBio::Tools::Run::StandAloneBlast - Object for the local execution of
the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is
experimental support for WU-Blast and NCBI rpsblast.
SYNOPSIS
# Local-blast "factory object" creation and blast-parameter
# initialization:
@params = (-database => 'swissprot', -outfile => 'blast1.out');
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
# Blast a sequence against a database:
$str = Bio::SeqIO->new(-file=>'t/amino.fa', -format => 'Fasta');
$input = $str->next_seq();
$input2 = $str->next_seq();
$blast_report = $factory->blastall($input);
# Run an iterated Blast (psiblast) of a sequence against a database:
$factory->j(3); # 'j' is blast parameter for # of iterations
$factory->outfile('psiblast1.out');
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$blast_report = $factory->blastpgp($input);
# Use blast to align 2 sequences against each other:
$factory = Bio::Tools::Run::StandAloneBlast->new(-outfile => 'bl2seq.out');
$factory->bl2seq($input, $input2);
# Experimental support for WU-Blast 2.0
my $factory = Bio::Tools::Run::StandAloneBlast->new(-program =>"wublastp",
-database =>"swissprot",
-e => 1e-20);
my $blast_report = $factory->wublast($seq);
# Experimental support for NCBI rpsblast
my $factory = Bio::Tools::Run::StandAloneBlast->new(-db => 'CDD/Cog',
-expect => 0.001);
$factory->F('T'); # turn on SEG filtering of query sequence
my $blast_report = $factory->rpsblast($seq);
# Use the experimental fast Blast parser, 'blast_pull'
my $factory = Bio::Tools::Run::StandAloneBlast->new(-_READMETHOD =>'blast_pull',
@other_params);
# Various additional options and input formats are available,
# see the DESCRIPTION section for details.
DESCRIPTION
This DESCRIPTION only documents Bio::Tools::Run::StandAloneBlast: - a
Bioperl object for running the NCBI standAlone BLAST package. Blast
itself, is a large & complex program - for more information regarding
BLAST, please see the BLAST documentation which accompanies the BLAST
distribution. BLAST is available from ftp://ncbi.nlm.nih.gov/blast/.
A source of confusion in documenting a BLAST interface is that the term
"program" is used in - at least - three different ways in the BLAST
documentation. In this DESCRIPTION, "program" will refer to the BLAST
routine set by the BLAST "-p" parameter that can be set to blastn,
blastp, tblastx etc. We will use the term Blast "executable" to refer
to the various different executable files that may be called - ie.
blastall, blastpgp or bl2seq. In addition, there are several BLAST
capabilities, which are also referred to as "programs", and are
implemented by using specific combinations of BLAST executables,
programs and parameters. They will be referred by their specific names
- eg PSIBLAST and PHIBLAST.
Before running StandAloneBlast it is necessary: to install BLAST on
your system, to edit set the environmental variable $BLASTDIR or your
$PATH variable to point to the BLAST directory, and to ensure that
users have execute privileges for the BLAST program.
If the databases which will be searched by BLAST are located in the
data subdirectory of the blast program directory (the default
installation location), StandAloneBlast will find them; however, if the
database files are located in any other location, environmental
variable $BLASTDATADIR will need to be set to point to that directory.
The use of the StandAloneBlast module is as follows: Initially, a local
blast "factory object" is created. The constructor may be passed an
optional array of (non-default) parameters to be used by the factory,
eg:
@params = (-program => 'blastn', -database => 'ecoli.nt');
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
Any parameters not explicitly set will remain as the defaults of the
BLAST executable. Note each BLAST executable has somewhat different
parameters and options. See the BLAST Documentation for a description
or run the BLAST executable from the command line followed solely with
a "-" to see a list of options and default values for that executable;
eg >blastall -.
BLAST parameters can be changed and/or examined at any time after the
factory has been created. The program checks that any parameter/switch
being set/read is valid. Except where specifically noted,
StandAloneBlast uses the same single-letter, case-sensitive parameter
names as the actual blast program. Currently no checks are included to
verify that parameters are of the proper type (e.g. string or numeric)
or that their values are within the proper range.
As an example, to change the value of the Blast parameter 'e' ('e' is
the parameter for expectation-value cutoff)
$expectvalue = 0.01;
$factory->e($expectvalue);
Note that for improved script readibility one can modify the name of
the (ncbi) BLAST parameters as desired as long as the initial letter
(and case) of the parameter are preserved, e.g.:
$factory->expectvalue($expectvalue);
Unfortunately, some of the BLAST parameters are not the single letter
one might expect (eg "iteration round" in blastpgp is 'j'). Again one
can check by using, for example:
> blastpgp -
Wublast parameters need to be complete (ie. don't truncate them to
their first letter), but are case-insensitive.
Once the factory has been created and the appropriate parameters set,
one can call one of the supported blast executables. The input
sequence(s) to these executables may be fasta file(s) as described in
the BLAST documentation.
$inputfilename = 't/testquery.fa';
$blast_report = $factory->blastall($inputfilename);
In addition, sequence input may be in the form of either a Bio::Seq
object or (a reference to) an array of Bio::Seq objects, e.g.:
$input = Bio::Seq->new(-id => "test query",
-seq => "ACTACCCTTTAAATCAGTGGGGG");
$blast_report = $factory->blastall($input);
NOTE: Use of the BPlite method has been deprecated and is no longer
supported.
For blastall and non-psiblast blastpgp runs, report object is
aBio::SearchIO object, selected by the user with the parameter
_READMETHOD. The leading underscore is needed to distinguish this
option from options which are passed to the BLAST executable. The
default parser is Bio::SearchIO::blast. In any case, the "raw" blast
report is also available. The filename is set by the 'outfile'
parameter and has the default value of "blastreport.out".
For psiblast execution in the BLAST "jumpstart" mode, the program must
be passed (in addition to the query sequence itself) an alignment
containing the query sequence (in the form of a SimpleAlign object) as
well as a "mask" specifying at what residues position-specific scoring
matrices (PSSMs) are to used and at what residues default scoring
matrices (eg BLOSUM) are to be used. See psiblast documentation for
more details. The mask itself is a string of 0's and 1's which is the
same length as each sequence in the alignment and has a "1" at
locations where (PSSMs) are to be used and a "0" at all other
locations. So for example:
$str = Bio::AlignIO->new(-file => "cysprot.msf",
-format => 'msf');
$aln = $str->next_aln();
$len = $aln->length_aln();
$mask = '1' x $len;
# simple case where PSSM's to be used at all residues
$report = $factory->blastpgp("cysprot1.fa", $aln, $mask);
For bl2seq execution, StandAloneBlast.pm can be combined with
AlignIO.pm to directly produce a SimpleAlign object from the alignment
of the two sequences produced by bl2seq as in:
# Get 2 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::Run::StandAloneBlast->new(-program => 'blastp',
-outfile => 'bl2seq.out');
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
# 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();
For more examples of syntax and use of StandAloneBlast.pm, the user is
encouraged to run the scripts standaloneblast.pl in the bioperl
examples/tools directory and StandAloneBlast.t in the bioperl t/
directory.
FEEDBACK
Mailing Lists
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
Support
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.
Reporting Bugs
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:
http://bugzilla.open-bio.org/
AUTHOR - Peter Schattner
Email schattner at alum.mit.edu
MAINTAINER - Torsten Seemann
Email torsten at infotech.monash.edu.au
CONTRIBUTORS
Sendu Bala bix@sendu.me.uk (reimplementation)
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Tools::Run::StandAloneBlast->new();
Function: Builds a newBio::Tools::Run::StandAloneBlast object
Returns : Bio::Tools::Run::StandAloneNCBIBlast or StandAloneWUBlast
Args : -quiet => boolean # make program execution quiet
-_READMETHOD => 'BLAST' (default, synonym 'SearchIO') || 'blast_pull'
# the parsing method, case insensitive
Essentially all BLAST parameters can be set via StandAloneBlast.pm.
Some of the most commonly used parameters are listed below. All
parameters have defaults and are optional except for -p in those
programs that have it. For a complete listing of settable parameters,
run the relevant executable BLAST program with the option "-" as in
blastall - Note that the input paramters (-i, -j, -input) should not be
set directly by you: this module sets them when you call one of the
executable methods.
Blastall
-p Program Name [String]
Input should be one of "blastp", "blastn", "blastx",
"tblastn", or "tblastx".
-d Database [String] default = nr
The database specified must first be formatted with formatdb.
Multiple database names (bracketed by quotations) will be accepted.
An example would be -d "nr est"
-e Expectation value (E) [Real] default = 10.0
-o BLAST report Output File [File Out] Optional,
default = ./blastreport.out ; set by StandAloneBlast.pm
-S Query strands to search against database (for blast[nx], and tblastx). 3 is both, 1 is top, 2 is bottom [Integer]
default = 3
Blastpgp (including Psiblast)
-j is the maximum number of rounds (default 1; i.e., regular BLAST)
-h is the e-value threshold for including sequences in the
score matrix model (default 0.001)
-c is the "constant" used in the pseudocount formula specified in the paper (default 10)
-B Multiple alignment file for PSI-BLAST "jump start mode" Optional
-Q Output File for PSI-BLAST Matrix in ASCII [File Out] Optional
rpsblast
-d Database [String] default = (none - you must specify a database)
The database specified must first be formatted with formatdb.
Multiple database names (bracketed by quotations) will be accepted.
An example would be -d "Cog Smart"
-e Expectation value (E) [Real] default = 10.0
-o BLAST report Output File [File Out] Optional,
default = ./blastreport.out ; set by StandAloneBlast.pm
Bl2seq
-p Program name: blastp, blastn, blastx. For blastx 1st argument should be nucleotide [String]
default = blastp
-o alignment output file [File Out] default = stdout
-e Expectation value (E) [Real] default = 10.0
-S Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom [Integer]
default = 3
WU-Blast
-p Program Name [String]
Input should be one of "wublastp", "wublastn", "wublastx",
"wutblastn", or "wutblastx".
-d Database [String] default = nr
The database specified must first be formatted with xdformat.
-E Expectation value (E) [Real] default = 10.0
-o BLAST report Output File [File Out] Optional,
default = ./blastreport.out ; set by StandAloneBlast.pm
executable
Title : executable
Usage : my $exe = $blastfactory->executable('blastall');
Function: Finds the full path to the executable
Returns : string representing the full path to the exe
Args : [optional] name of executable to set path to
[optional] boolean flag whether or not warn when exe is not found
program_dir
Title : program_dir
Usage : my $dir = $factory->program_dir();
Function: Abstract get method for dir of program.
Returns : string representing program directory
Args : none
_setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file(s) for Blast executable
Example :
Returns : name of file containing Blast data input
Args : Seq object reference or input file name
Bio::Tools::Run::WrapperBase methods
no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_name
Title : outfile_name
Usage : my $outfile = $tcoffee->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanup
Title : cleanup
Usage : $tcoffee->cleanup();
Function: Will cleanup the tempdir directory after a PAML run
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none
perl v5.14.12011-07-2Bio::Tools::Run::StandAloneBlast(3)