NAME¶
Bio::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:
https://redmine.open-bio.org/projects/bioperl/
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 parameters (-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
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
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
Title : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none