Provided by: libbio-perl-run-perl_1.7.1-3_all 
NAME
Bio::Tools::Run::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*
SYNOPSIS
NOTE: This module is related to the Bio::Tools::Run::StandAloneBlast system in name (and
inspiration) only. You must use this module directly.
# existing blastdb:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb'
);
# create blastdb from fasta file and attach
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => 'myseqs.fas',
-create => 1
);
# create blastdb from BioPerl sequence collection objects
$alnio = Bio::AlignIO->new( -file => 'alignment.msf' );
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => $alnio,
-create => 1
);
@seqs = $alnio->next_aln->each_seq;
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => \@seqs,
-create => 1
);
# create database with masks
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'my_masked_db',
-db_data => 'myseqs.fas',
-masker => 'dustmasker',
-mask_data => 'maskseqs.fas',
-create => 1
);
# create a mask datafile separately
$mask_file = $fac->make_mask(
-data => 'maskseqs.fas',
-masker => 'dustmasker'
);
# query database for metadata
$info_hash = $fac->db_info;
$num_seq = $fac->db_num_sequences;
@mask_metadata = @{ $fac->db_filter_algorithms };
# perform blast methods
$result = $fac->tblastn( -query => $seqio );
# see Bio::Tools::Run::StandAloneBlastPlus::BlastMethods
# for many more details
DESCRIPTION
NOTE: This module requires BLAST+ v. 2.2.24+ and higher. Until the API stabilizes for
BLAST+, consider this module highly experimental.
This module along with Bio::Tools::Run::StandAloneBlastPlus::BlastMethods allows the user
to perform BLAST functions using the external program suite "blast+" (available at
<ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/>), using BioPerl objects and
Bio::SearchIO facilities. This wrapper can prepare BLAST databases as well as run BLAST
searches. It can also be used to run "blast+" programs independently.
This module encapsulates object construction and production of databases and masks. Blast
analysis methods ("blastp, psiblast", etc>) are contained in
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.
USAGE
The basic mantra is to (1) create a BlastPlus factory using the "new()" constructor, and
(2) perform BLAST analyses by calling the desired BLAST program by name off the factory
object. The blast database itself and any masking data are attached to the factory object
(step 1). Query sequences and any parameters associated with particular programs are
provided to the blast method call (step 2), and are run against the attached database.
Factory construction/initialization
The factory needs to be told where the blast+ programs live. The "BLASTPLUSDIR"
environment variable will be checked for the default executable directory. The program
directory can be set for individual factory instances with the "PROG_DIR" parameter. All
the blast+ programs must be accessible from that directory (i.e., as executable files or
symlinks).
Either the database or BLAST subject data must be specified at object construction.
Databases can be pre-existing formatted BLAST dbs, or can be built directly from fasta
sequence files or BioPerl sequence object collections of several kinds. The key
constructor parameters are "DB_NAME", "DB_DATA", "DB_DIR".
To specify a pre-existing BLAST database, use "DB_NAME" alone:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => 'mydb'
);
The directory can be specified along with the basename, or separately with "DB_DIR":
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => '~/home/blast/mydb'
);
#same as
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => 'mydb', -DB_DIR => '~/home/blast'
);
To create a BLAST database de novo, see "Creating a BLAST database".
If you wish to apply pre-existing mask data (i.e., the final ASN1 output from one of the
blast+ masker programs), to the database before querying, specify it with "MASK_FILE":
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => 'mydb', -MASK_FILE => 'mymaskdata.asn'
);
Creating a BLAST database
There are several options for creating the database de novo using attached data, both
before and after factory construction. If a temporary database (one that can be deleted by
the "cleanup()" method) is desired, leave out the "-db_name" parameter. If "-db_name" is
specified, the database will be preserved with the basename specified.
Use "-create =" 1> to create a new database (otherwise the factory will look for an
existing database). Use "-overwrite =" 1> to create and overwrite an existing database.
Note that the database is not created immediately on factory construction. It will be
created if necessary on the first use of a factory BLAST method, or you can force database
creation by executing
$fac->make_db();
• Specify data during construction
With a FASTA file:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => 'myseqs.fas',
-create => 1
);
With another BioPerl object collection:
$alnio = Bio::AlignIO->new( -file => 'alignment.msf' );
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => $alnio,
-create => 1
);
@seqs = $alnio->next_aln->each_seq;
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'mydb',
-db_data => \@seqs,
-create => 1
);
Other collections (e.g., Bio::SeqIO) are valid. If a certain type does not work,
please submit an enhancement request.
To create temporary databases, leave out the "-db_name", e.g.
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_data => 'myseqs.fas',
-create => 1
);
To get the tempfile basename, do:
$dbname = $fac->db;
• Specify data post-construction
Use the explicit attribute setters:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-create => 1
);
$fac->set_db_data('myseqs.fas');
$fac->make_db;
Creating and using mask data
The blast+ mask utilities "windowmasker", "segmasker", and "dustmasker" are available.
Masking can be rolled into database creation, or can be executed later. If your mask data
is already created and in ASN1 format, set the "-mask_file" attribute on construction (see
"Factory constuction/initialization").
To create a mask from raw data or an existing database and apply the mask upon database
creation, construct the factory like so:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'my_masked_db',
-db_data => 'myseqs.fas',
-masker => 'dustmasker',
-mask_data => 'maskseqs.fas',
-create => 1
);
The masked database will be created during "make_db".
The "-mask_data" parameter can be a FASTA filename or any BioPerl sequence object
collection. If the datatype ('nucl' or 'prot') of the mask data is not compatible with the
selected masker, an exception will be thrown with a message to that effect.
To create a mask ASN1 file that can be used in the "-mask_file" parameter separately from
the attached database, use the "make_mask()" method directly:
$mask_file = $fac->make_mask(-data => 'maskseqs.fas',
-masker => 'dustmasker');
# segmasker can use a blastdb as input
$mask_file = $fac->make_mask(-mask_db => 'mydb',
-masker => 'segmasker')
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'my_masked_db',
-db_data => 'myseqs.fas',
-mask_file => $mask_file
-create => 1
);
Getting database information
To get a hash containing useful metadata on an existing database (obtained by running
"blastdbcmd -info", use "db_info()":
# get info on the attached database..
$info = $fac->db_info;
# get info on another database
$info = $fac->db_info('~/home/blastdbs/another');
To get a particular info element for the attached database, just call the element name off
the factory:
$num_seqs = $fac->db_num_sequences;
# info on all the masks applied to the db, if any:
@masking_info = @{ $fac->db_filter_algorithms };
Accessing the Bio::Tools::Run::BlastPlus factory
The blast+ programs are actually executed by a Bio::Tools::Run::BlastPlus wrapper
instance. This instance is available for peeking and poking in the StandAloneBlastPlus
"factory()" attribute. For convenience, "BlastPlus" methods can be run from the
"StandAloneBlastPlus" object, and are delegated to the "factory()" attribute. For example,
to get the blast+ program to be executed, examine either
$fac->factory->command
or
$fac->command
Similarly, the current parameters for the "BlastPlus" factory are
@parameters = $fac->get_parameters
Cleaning up temp files
Temporary analysis files produced under a single factory instances can be unlinked by
running
$fac->cleanup;
Tempfiles are generally not removed unless this method is explicitly called. "cleanup()"
only unlinks "registered" files and databases. All temporary files are automatically
registered; in particular, "anonymous" databases (such as
$fac->Bio::Tools::Run::StandAloneBlastPlus->new(
-db_data => 'myseqs.fas',
-create => 1
);
without a "-db_name" specification) are registered for cleanup. Any file or database can
be registered with an internal method:
$fac->_register_temp_for_cleanup('testdb');
Other Goodies
• You can check whether a given basename points to a properly formatted BLAST database
by doing
$is_good = $fac->check_db('putative_db');
• User parameters can be passed to the underlying blast+ programs (if you know what
you're doing) with "db_make_args" and "mask_make_args":
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_name => 'customdb',
-db_data => 'myseqs.fas',
-db_make_args => [ '-taxid_map' => 'seq_to_taxa.txt' ],
-masker => 'windowmasker',
-mask_data => 'myseqs.fas',
-mask_make_args => [ '-dust' => 'T' ],
-create => 1
);
• You can prevent exceptions from being thrown by failed blast+ program executions by
setting "no_throw_on_crash". Examine the error with "stderr()":
$fac->no_throw_on_crash(1);
$fac->make_db;
if ($fac->stderr =~ /Error:/) {
#handle error
...
}
SEE ALSO
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods, Bio::Tools::Run::BlastPlus
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 the Bioperl mailing list. 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 of the bugs and their
resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
CONTRIBUTORS
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 = new Bio::Tools::Run::StandAloneBlastPlus();
Function: Builds a new Bio::Tools::Run::StandAloneBlastPlus object
Returns : an instance of Bio::Tools::Run::StandAloneBlastPlus
Args : named argument (key => value) pairs:
-db : blastdb name
db()
Title : db
Usage : $obj->db($newval)
Function: contains the basename of the local blast database
Example :
Returns : value of db (a scalar string)
Args : readonly
factory()
Title : factory
Usage : $obj->factory($newval)
Function: attribute containing the Bio::Tools::Run::BlastPlus
factory
Example :
Returns : value of factory (Bio::Tools::Run::BlastPlus object)
Args : readonly
program_version()
Title : program_version
Usage : $version = $bedtools_fac->program_version()
Function: Returns the program version (if available)
Returns : string representing location and version of the program
Note : this works around the WrapperBase::version() method conflicting with
the -version parameter for SABlast (good argument for not having
getter/setters for these)
package_version()
Title : package_version
Usage : $version = $bedtools_fac->package_version()
Function: Returns the BLAST+ package version (if available)
Returns : string representing BLAST+ package version (may differ from version())
DB methods
make_db()
Title : make_db
Usage :
Function: create the blast database (if necessary),
imposing masking if specified
Returns : true on success
Args :
make_mask()
Title : make_mask
Usage :
Function: create masking data based on specified parameters
Returns : mask data filename (scalar string)
Args :
db_info()
Title : db_info
Usage :
Function: get info for database
(via blastdbcmd -info); add factory attributes
Returns : hash of database attributes
Args : [optional] db name (scalar string) (default: currently attached db)
set_db_make_args()
Title : set_db_make_args
Usage :
Function: set the DB make arguments attribute
with checking
Returns : true on success
Args : arrayref or hashref of named arguments
set_mask_make_args()
Title : set_mask_make_args
Usage :
Function: set the masker make arguments attribute
with checking
Returns : true on success
Args : arrayref or hasref of named arguments
check_db()
Title : check_db
Usage :
Function: determine if database with registered name and dir
exists
Returns : 1 if db present, 0 if not present, undef if name/dir not
set
Args : [optional] db name (default is 'registered' name in $self->db)
[optional] db directory (default is 'registered' dir in
$self->db_dir)
no_throw_on_crash()
Title : no_throw_on_crash
Usage : $fac->no_throw_on_crash($newval)
Function: set to prevent an exeception throw on a failed
blast program execution
Example :
Returns : value of no_throw_on_crash (boolean)
Args : on set, new value (boolean)
Internals
_fastize()
Title : _fastize
Usage :
Function: convert a sequence collection to a temporary
fasta file (sans gaps)
Returns : fasta filename (scalar string)
Args : sequence collection
_register_temp_for_cleanup()
Title : _register_temp_for_cleanup
Usage :
Function: register a file for cleanup with
cleanup() method
Returns : true on success
Args : a file name or a blastdb basename
(scalar string)
cleanup()
Title : cleanup
Usage :
Function: unlink files registered for cleanup
Returns : true on success
Args :
AUTOLOAD
In this module, "AUTOLOAD()" delegates Bio::Tools::Run::WrapperBase and
Bio::Tools::Run::WrapperBase::CommandExts methods (including those of Bio::ParamterBaseI)
to the "factory()" attribute:
$fac->stderr
gives you
$fac->factory->stderr
If $AUTOLOAD isn't pointing to a WrapperBase method, then AUTOLOAD attempts to return a
"db_info" attribute: e.g.
$fac->db_num_sequences
works by looking in the $fac->db_info() hash.
Finally, if $AUTOLOAD is pointing to a blast query method, AUTOLOAD runs "run" with the
"-method" parameter appropriately set.