# $Id$
#
# BioPerl module for Bio::Tools::Run::StandAloneBlastPlus
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*
=head1 SYNOPSIS
B<NOTE>: This module is related to the
L<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
=head1 DESCRIPTION
B<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
L<Bio::Tools::Run::StandAloneBlastPlus::BlastMethods> allows the user
to perform BLAST functions using the external program suite C<blast+>
(available at
L<ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/>), using
BioPerl objects and L<Bio::SearchIO> facilities. This wrapper can
prepare BLAST databases as well as run BLAST searches. It can also be
used to run C<blast+> programs independently.
This module encapsulates object construction and production of
databases and masks. Blast analysis methods (C<blastp, psiblast>,
etc>) are contained in
L<Bio::Tools::Run::StandAloneBlastPlus::BlastMethods>.
=head1 USAGE
The basic mantra is to (1) create a BlastPlus factory using the
C<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.
=head2 Factory construction/initialization
The factory needs to be told where the blast+ programs live. The
C<BLASTPLUSDIR> environment variable will be checked for the default
executable directory. The program directory can be set for individual
factory instances with the C<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 C<DB_NAME>, C<DB_DATA>, C<DB_DIR>.
To specify a pre-existing BLAST database, use C<DB_NAME> alone:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => 'mydb'
);
The directory can be specified along with the basename, or separately
with C<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 L</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 C<MASK_FILE>:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-DB_NAME => 'mydb', -MASK_FILE => 'mymaskdata.asn'
);
=head2 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 C<cleanup()>
method) is desired, leave out the C<-db_name> parameter. If
C<-db_name> is specified, the database will be preserved with the
basename specified.
Use C<-create => 1> to create a new database (otherwise the factory
will look for an existing database). Use C<-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();
=over
=item * 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., L<Bio::SeqIO>) are valid. If a certain type
does not work, please submit an enhancement request.
To create temporary databases, leave out the C<-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;
=item * Specify data post-construction
Use the explict attribute setters:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-create => 1
);
$fac->set_db_data('myseqs.fas');
$fac->make_db;
=back
=head2 Creating and using mask data
The blast+ mask utilities C<windowmasker>, C<segmasker>, and
C<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 C<-mask_file> attribute on
construction (see L</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 C<make_db>.
The C<-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 C<-mask_file>
parameter separately from the attached database, use the
C<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
);
=head2 Getting database information
To get a hash containing useful metadata on an existing database
(obtained by running C<blastdbcmd -info>, use C<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 };
=head2 Accessing the L<Bio::Tools::Run::BlastPlus> factory
The blast+ programs are actually executed by a
L<Bio::Tools::Run::BlastPlus> wrapper instance. This instance is
available for peeking and poking in the L<StandAloneBlastPlus>
C<factory()> attribute. For convenience, C<BlastPlus> methods can be
run from the C<StandAloneBlastPlus> object, and are delegated to the
C<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 C<BlastPlus> factory are
@parameters = $fac->get_parameters
=head2 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. C<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 C<-db_name> specification) are registered for cleanup. Any
file or database can be registered with an internal method:
$fac->_register_temp_for_cleanup('testdb');
=head2 Other Goodies
=over
=item
You can check whether a given basename points to a properly formatted
BLAST database by doing
$is_good = $fac->check_db('putative_db');
=item
User parameters can be passed to the underlying blast+ programs (if
you know what you're doing) with C<db_make_args> and C<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
);
=item
You can prevent exceptions from being thrown by failed blast+ program
executions by setting C<no_throw_on_crash>. Examine the error with
C<stderr()>:
$fac->no_throw_on_crash(1);
$fac->make_db;
if ($fac->stderr =~ /Error:/) {
#handle error
...
}
=back
=head1 SEE ALSO
L<Bio::Tools::Run::StandAloneBlastPlus::BlastMethods>,
L<Bio::Tools::Run::BlastPlus>
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<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.
=head2 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/
=head1 AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
=head1 CONTRIBUTORS
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::StandAloneBlastPlus;
use strict;
our $AUTOLOAD;
# Object preamble - inherits from Bio::Root::Root
use lib '../../..';
use Bio::Root::Root;
use Bio::SeqIO;
use Bio::Tools::GuessSeqFormat;
use Bio::Tools::Run::StandAloneBlastPlus::BlastMethods;
use File::Temp 0.22;
use IO::String;
use base qw(Bio::Root::Root);
unless ( eval "require Bio::Tools::Run::BlastPlus" ) {
Bio::Root::Root->throw("This module requires 'Bio::Tools::Run::BlastPlus'");
}
my %AVAILABLE_MASKERS = (
'windowmasker' => 'nucl',
'dustmasker' => 'nucl',
'segmasker' => 'prot'
);
my %MASKER_ENCODING = (
'windowmasker' => 'maskinfo_asn1_text',
'dustmasker' => 'maskinfo_asn1_text',
'segmasker' => 'maskinfo_asn1_text'
);
my $bp_class = 'Bio::Tools::Run::BlastPlus';
# what's the desire here?
#
# * factory object (created by new())
# - points to some blast db entity, so all functions run off the
# the factory (except bl2seq?) use the associated db
#
# * create a blast formatted database:
# - specify a file, or an AlignI object
# - store for later, or store in a tempfile to throw away
# - object should store its own database pointer
# - provide masking options based on the maskers provided
#
# * perform database actions via db-oriented blast+ commands
# via the object
#
# * perform blast searches against the database
# - blastx, blastp, blastn, tblastx, tblastn
# - specify Bio::Seq objects or files as queries
# - output the results as a file or as a Bio::Search::Result::BlastResult
# * perform 'special' (i.e., ones I don't know) searches
# - psiblast, megablast, rpsblast, rpstblastn
# some of these are "tasks" under particular programs
# check out psiblast, why special (special 'iteration' handling in
# ...::BlastResult)
# check out rpsblast, megablast
#
# * perform bl2seq
# - return the alignment directly as a convenience, using Bio::Search
# functions
# lazy db formatting: makeblastdb only on first blast request...
# ParameterBaseI delegation : use AUTOLOAD
#
#
=head2 new
Title : new
Usage : my $obj = new Bio::Tools::Run::StandAloneBlastPlus();
Function: Builds a new Bio::Tools::Run::StandAloneBlastPlus object
Returns : an instance of Bio::Tools::Run::StandAloneBlastPlus
Args : named argument (key => value) pairs:
-db : blastdb name
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($db_name, $db_data, $db_dir, $db_make_args,
$mask_file, $mask_data, $mask_make_args, $masker,
$create, $overwrite, $is_remote, $prog_dir, $program_dir)
= $self->_rearrange([qw(
DB_NAME
DB_DATA
DB_DIR
DB_MAKE_ARGS
MASK_FILE
MASK_DATA
MASK_MAKE_ARGS
MASKER
CREATE
OVERWRITE
REMOTE
PROG_DIR
PROGRAM_DIR
)], @args);
# parm taint checks
if ($db_name) {
$self->throw("DB name contains invalid characters") unless $db_name =~ m{^[a-z0-9_/:.+-]+$}i;
}
if ( $db_dir ) {
$self->throw("DB directory (DB_DIR) not found") unless (-d $db_dir);
$self->{'_db_dir'} = $db_dir;
}
else {
$self->{'_db_dir'} = '.';
}
$program_dir ||= $prog_dir; # alias
# now handle these systematically (bug #3003)
# allow db_name to include path info
# let db_dir act as root if present and db_name is a relative path
# db property contains the pathless name only
if ($db_name) {
my ($v,$d,$f) = File::Spec->splitpath($db_name);
$self->throw("No DB name at the end of path '$db_name'") unless $f;
$f =~ s/\..*$//; # tolerant of extensions, but ignore them
$self->{_db} = $f;
# now establish db_path property as the internal authority on
# db location...
if ( File::Spec->file_name_is_absolute($db_name) ) {
$self->throw("Path specified in DB name ('$d') does not exist") unless !$d || (-d $d);
$self->{_db_path} = File::Spec->catfile($d,$f);
$self->{_db_dir} = $d;
# ignore $db_dir, give heads-up
$self->warn("DB name is an absolute path; setting db_dir to '".$self->db_dir."'") if $db_dir;
}
else {
$d = File::Spec->catdir($self->db_dir, $d);
$self->throw("Path specified by DB_DIR+DB_NAME ('$d') does not exist") unless !$d || (-d $d);
$self->{_db_path} = File::Spec->catfile($d,$f);
}
}
if ($masker) {
$self->throw("Masker '$masker' not available") unless
grep /^$masker$/, keys %AVAILABLE_MASKERS;
$self->{_masker} = $masker;
}
if ($program_dir) {
$self->throw("Can't find program directory '$program_dir'") unless
-d $program_dir;
$self->{_program_dir} = $program_dir;
}
elsif ($ENV{BLASTPLUSDIR}) {
$self->{_program_dir} = $ENV{BLASTPLUSDIR};
}
$Bio::Tools::Run::BlastPlus::program_dir = $self->{_program_dir} ||
$Bio::Tools::Run::BlastPlus::program_dir;
$self->set_db_make_args( $db_make_args) if ( $db_make_args );
$self->set_mask_make_args( $mask_make_args) if ($mask_make_args);
$self->{'_create'} = $create;
$self->{'_overwrite'} = $overwrite;
$self->{'_is_remote'} = $is_remote;
$self->{'_db_data'} = $db_data;
$self->{'_mask_file'} = $mask_file;
$self->{'_mask_data'} = $mask_data;
# check db
if (defined $self->check_db and $self->check_db == 0 and !$self->is_remote) {
$self->throw("DB '".$self->db."' can't be found. To create, set -create => 1.") unless ($create || $overwrite);
}
if (!$self->db) {
# allow this to pass; catch lazily at make_db...
if (!$self->db_data) {
$self->debug('No database or db data specified. '.
'To create a new database, provide '.
'-db_data => [fasta|\@seqs|$seqio_object]')
}
# no db specified; create temp db
$self->{_create} = 1;
if ($self->db_dir) {
my $fh = File::Temp->new(TEMPLATE => 'DBXXXXX',
DIR => $self->db_dir,
UNLINK => 1);
my ($v,$d,$f) = File::Spec->splitpath($fh->filename);
$self->{_db} = $f;
$self->{_db_path} = $fh->filename;
$self->_register_temp_for_cleanup($self->db_path);
$fh->close;
}
else {
$self->{_db_dir} = File::Temp->newdir('DBDXXXXX');
$self->{_db} = 'DBTEMP';
$self->{_db_path} = File::Spec->catfile($self->db_dir,
$self->db);
}
}
return $self;
}
=head2 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
=cut
sub db { shift->{_db} }
sub db_name { shift->{_db} }
sub set_db_name { shift->{_db} = shift }
sub db_dir { shift->{_db_dir} }
sub set_db_dir { shift->{_db_dir} = shift }
sub db_path { shift->{_db_path} }
sub db_data { shift->{_db_data} }
sub set_db_data { shift->{_db_data} = shift }
sub db_type { shift->{_db_type} }
sub masker { shift->{_masker} }
sub set_masker { shift->{_masker} = shift }
sub mask_file { shift->{_mask_file} }
sub set_mask_file { shift->{_mask_file} = shift }
sub mask_data { shift->{_mask_data} }
sub set_mask_data { shift->{_mask_data} = shift }
=head2 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
=cut
sub factory { shift->{_factory} }
sub create { shift->{_create} }
sub overwrite { shift->{_overwrite} }
sub is_remote { shift->{_is_remote} }
=head2 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)
=cut
=head2 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())
=cut
sub program_version {
my $self = shift;
my $fac = $self->factory;
$fac->program_version(@_) if $fac;
}
sub package_version {
my $self = shift;
my $fac = $self->factory;
$fac->package_version(@_) if $fac;
}
=head1 DB methods
=head2 make_db()
Title : make_db
Usage :
Function: create the blast database (if necessary),
imposing masking if specified
Returns : true on success
Args :
=cut
# should also provide facility for creating subdatabases from
# existing databases (i.e., another format for $data: the name of an
# existing blastdb...)
sub make_db {
my $self = shift;
my @args = @_;
return 1 if ( $self->check_db && !$self->overwrite ); # already there or force make
$self->throw('No database or db data specified. '.
'To create a new database, provide '.
'-db_data => [fasta|\@seqs|$seqio_object]')
unless $self->db_data;
# db_data can be: fasta file, array of seqs, Bio::SeqIO object
my $data = $self->db_data;
$data = $self->_fastize($data);
my $testio = Bio::SeqIO->new(-file=>$data, -format=>'fasta');
$self->{_db_type} = ($testio->next_seq->alphabet =~ /.na/) ? 'nucl' : 'prot';
$testio->close;
my ($v,$d,$name) = File::Spec->splitpath($data);
$name =~ s/\.fas$//;
$self->{_db} ||= $name;
$self->{_db_path} = File::Spec->catfile($self->db_dir,$self->db);
# <#######[
# deal with creating masks here,
# and provide correct parameters to the
# makeblastdb ...
# accomodate $self->db_make_args here -- allow them
# to override defaults, or allow only those args
# that are not specified here?
my $usr_db_args ||= $self->db_make_args;
my %usr_args = @$usr_db_args if $usr_db_args;
my %db_args = (
-in => $data,
-dbtype => $self->db_type,
-out => $self->db_path,
-title => $self->db,
-parse_seqids => 1 # necessary for masking
);
# usr arg override
if (%usr_args) {
$db_args{$_} = $usr_args{$_} for keys %usr_args;
}
# do masking if requested
# if the (masker and mask_data) OR mask_file attributes of this
# object are set, assume that masking is desired
#
if ($self->mask_file) { # the actual masking data is provided
$db_args{'-mask_data'} = $self->mask_file;
}
elsif ($self->masker && $self->mask_data) { # build the mask
$db_args{'-mask_data'} = $self->make_mask(-data => $self->mask_data);
$self->throw("Masker error: message is '".$self->stderr."'") unless
$db_args{'-mask_data'};
$self->{_mask_data} = $db_args{'-mask_data'};
}
$self->{_factory} = $bp_class->new(
-command => 'makeblastdb',
%db_args
);
$self->factory->no_throw_on_crash($self->no_throw_on_crash);
return $self->factory->_run;
}
=head2 make_mask()
Title : make_mask
Usage :
Function: create masking data based on specified parameters
Returns : mask data filename (scalar string)
Args :
=cut
# mask program usage (based on blast+ manual)
#
# program dbtype opn
# windowmasker nucl mask overrep data, low-complexity (optional)
# dustmasker nucl mask low-complexity
# segmasker prot
sub make_mask {
my $self = shift;
my @args = @_;
my ($data, $mask_db, $make_args, $masker) = $self->_rearrange([qw(
DATA
MASK_DB
MAKE_ARGS
MASKER)], @args);
my (%mask_args,%usr_args,$db_type);
my $infmt = 'fasta';
$self->throw("make_mask requires -data argument") unless $data;
$masker ||= $self->masker;
$self->throw("no masker specified and no masker default set in object")
unless $masker;
my $usr_make_args ||= $self->mask_make_args;
%usr_args = @$usr_make_args if $usr_make_args;
unless (grep /^$masker$/, keys %AVAILABLE_MASKERS) {
$self->throw("Masker '$masker' not available");
}
if ($self->check_db($data)) {
unless ($masker eq 'segmasker') {
$self->throw("Masker '$masker' can't use a blastdb as primary input");
}
unless ($self->db_info($data)->{_db_type} eq
$AVAILABLE_MASKERS{$masker}) {
$self->throw("Masker '$masker' is incompatible with input db sequence type");
}
$infmt = 'blastdb';
}
else {
$data = $self->_fastize($data);
my $sio = Bio::SeqIO->new(-file=>$data);
my $s = $sio->next_seq;
my $type;
if ($s->alphabet =~ /.na/) {
$type = 'nucl';
}
elsif ($s->alphabet =~ /protein/) {
$type = 'prot';
}
else {
$type = 'UNK';
}
unless ($type eq $AVAILABLE_MASKERS{$masker}) {
$self->throw("Masker '$masker' is incompatible with sequence type '$type'");
}
}
# check that sequence type and masker program match:
# now, need to provide reasonable default masker arg settings,
# and override these with $usr_make_args as necessary and appropriate
my $mh = File::Temp->new(TEMPLATE=>'MSKXXXXX',
UNLINK => 0,
DIR => $self->db_dir);
my $mask_outfile = $mh->filename;
$mh->close;
$self->_register_temp_for_cleanup(File::Spec->catfile($self->db_dir,$mask_outfile));
%mask_args = (
-in => $data,
-parse_seqids => 1,
#-outfmt => $MASKER_ENCODING{$masker}
);
# usr arg override
if (%usr_args) {
$mask_args{$_} = $usr_args{$_} for keys %usr_args;
}
# masker-specific pipelines
my $status;
for ($masker) {
m/dustmasker/ && do {
$mask_args{'-out'} = $mask_outfile;
$self->{_factory} = $bp_class->new(-command => $masker,
%mask_args);
$self->factory->no_throw_on_crash($self->no_throw_on_crash);
$status = $self->factory->_run;
last;
};
m/windowmasker/ && do {
# check mask_db if present
if ($mask_db) {
unless ($self->check_db($mask_db)) {
$self->throw("Mask database '$mask_db' is not present or valid");
}
}
my $cth = File::Temp->new(TEMPLATE=>'MCTXXXXX',
DIR => $self->db_dir);
my $ct_file = $cth->filename;
$cth->close;
$mask_args{'-out'} = $ct_file;
$mask_args{'-mk_counts'} = 'true';
$self->{_factory} = $bp_class->new(-command => $masker,
%mask_args);
$self->factory->no_throw_on_crash($self->no_throw_on_crash);
$status = $self->factory->_run;
last unless $status;
delete $mask_args{'-mk_counts'};
$mask_args{'-ustat'} = $ct_file;
$mask_args{'-out'} = $mask_outfile;
if ($mask_db) {
$mask_args{'-in'} = $mask_db;
$mask_args{'-infmt'} = 'blastdb';
}
$self->factory->reset_parameters(%mask_args);
$self->factory->no_throw_on_crash($self->no_throw_on_crash);
$status = $self->factory->_run;
last;
};
m/segmasker/ && do {
$mask_args{'-infmt'} = $infmt;
$mask_args{'-out'} = $mask_outfile;
$self->{_factory} = $bp_class->new(-command => $masker,
%mask_args);
$self->factory->no_throw_on_crash($self->no_throw_on_crash);
$status = $self->factory->_run;
last;
};
do {
$self->throw("Masker program '$masker' not recognized");
};
}
return $status ? $mask_outfile : $status;
}
=head2 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)
=cut
sub db_info {
my $self = shift;
my $db = shift;
$db ||= $self->db_path;
unless ($db) {
$self->warn("db_info: db not specified and no db attached");
return;
}
if ($self->is_remote) {
$self->warn("db_info: sorry, can't get info for remote database (complain to NCBI)");
return;
}
if ($db eq $self->db and $self->{_db_info}) {
return $self->{_db_info}; # memoized
}
my $db_info_text;
$self->{_factory} = $bp_class->new( -command => 'blastdbcmd',
-info => 1,
-db => $db );
$self->factory->no_throw_on_crash(1);
$self->factory->_run();
$self->factory->no_throw_on_crash(0);
if ($self->factory->stderr =~ /No alias or index file found/) {
$self->warn("db_info: Couldn't find database ".$self->db."; make with make_db()");
return;
}
$db_info_text = $self->factory->stdout;
# parse info into attributes
my $infh = IO::String->new($db_info_text);
my %attr;
while (<$infh>) {
/Database: (.*)/ && do {
$attr{db_info_name} = $1;
next;
};
/([0-9,]+) sequences; ([0-9,]+) total/ && do {
$attr{db_num_sequences} = $1;
$attr{db_total_bases} = $2;
$attr{db_num_sequences} =~ s/,//g;
$attr{db_total_bases} =~ s/,//g;
next;
};
/Date: (.*?)\s+Longest sequence: ([0-9,]+)/ && do {
$attr{db_date} = $1; # convert to more usable date object
$attr{db_longest_sequence} = $2;
$attr{db_longest_sequence} =~ s/,//g;
next;
};
/Algorithm ID/ && do {
my $alg = $attr{db_filter_algorithms} = [];
while (<$infh>) {
if (/\s+([0-9]+)\s+([a-z0-9_]+)\s+(.*)/i) {
push @$alg, { algorithm_id => $1,
algorithm_name => $2,
algorithm_opts => $3 };
}
else {
last;
}
}
next;
};
}
# get db type
if ( -e $db.'.psq' ) {
$attr{_db_type} = 'prot';
}
elsif (-e $db.'.nsq') {
$attr{_db_type} = 'nucl';
}
else {
$attr{_db_type} = 'UNK'; # bork
}
if ($db eq $self->db) {
$self->{_db_type} = $attr{_db_type};
$self->{_db_info_text} = $db_info_text;
$self->{_db_info} = \%attr;
}
return \%attr;
}
=head2 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
=cut
sub set_db_make_args {
my $self = shift;
my $args = shift;
$self->throw("Arrayref or hashref required at DB_MAKE_ARGS") unless
ref($args) =~ /^ARRAY|HASH$/;
if (ref($args) eq 'HASH') {
my @a = %$args;
$args = \@a;
}
$self->throw("Named args required for DB_MAKE_ARGS") unless !(@$args % 2);
$self->{'_db_make_args'} = $args;
return 1;
}
sub db_make_args { shift->{_db_make_args} }
=head2 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
=cut
sub set_mask_make_args {
my $self = shift;
my $args = shift;
$self->throw("Arrayref or hashref required at MASK_MAKE_ARGS") unless
ref($args) =~ /^ARRAY|HASH$/;
if (ref($args) eq 'HASH') {
my @a = %$args;
$args = \@a;
}
$self->throw("Named args required at MASK_MAKE_ARGS") unless !(@$args % 2);
$self->{'_mask_make_args'} = $args;
return 1;
}
sub mask_make_args { shift->{_mask_make_args} }
=head2 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)
=cut
sub check_db {
my $self = shift;
my ($db) = @_;
my $db_path;
if ($db) {
my ($v,$d,$f) = File::Spec->splitpath($db);
$f =~ s/\..*$//; # ignore extensions
$db_path = File::Spec->catfile($d||'.',$f);
}
else {
$db_path = $self->db_path;
}
if ( $db_path ) {
$self->{_factory} = $bp_class->new( -command => 'blastdbcmd',
-info => 1,
-db => $db_path );
# $DB::single=1;
$self->factory->no_throw_on_crash(1);
$self->factory->_run();
$self->factory->no_throw_on_crash(0);
return 0 if ($self->factory->stderr =~ /No alias or index file found/);
return 1;
}
return;
}
=head2 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)
=cut
sub no_throw_on_crash {
my $self = shift;
return $self->{'no_throw_on_crash'} = shift if @_;
return $self->{'no_throw_on_crash'};
}
=head1 Internals
=head2 _fastize()
Title : _fastize
Usage :
Function: convert a sequence collection to a temporary
fasta file (sans gaps)
Returns : fasta filename (scalar string)
Args : sequence collection
=cut
sub _fastize {
my $self = shift;
my $data = shift;
for ($data) {
!ref && do {
# suppose a fasta file name
$self->throw('Sequence file not found') unless -e $data;
my $guesser = Bio::Tools::GuessSeqFormat->new(-file => $data);
$self->throw('Sequence file not in FASTA format') unless
$guesser->guess eq 'fasta';
last;
};
(ref eq 'ARRAY') && (ref $$data[0]) &&
($$data[0]->isa('Bio::Seq') || $$data[0]->isa('Bio::PrimarySeq'))
&& do {
my $fh = File::Temp->new(TEMPLATE => 'DBDXXXXX',
UNLINK => 0,
DIR => $self->db_dir,
SUFFIX => '.fas');
my $fname = $fh->filename;
$fh->close;
$self->_register_temp_for_cleanup($fname);
my $fasio = Bio::SeqIO->new(-file=>">$fname", -format=>"fasta")
or $self->throw("Can't create temp fasta file");
for (@$data) {
my $s = $_->seq;
my $a = $_->alphabet;
$s =~ s/[$Bio::PrimarySeq::GAP_SYMBOLS]//g;
$_->seq( $s );
$_->alphabet($a);
$fasio->write_seq($_);
}
$fasio->close;
$data = $fname;
last;
};
ref && do { # some kind of object
my ($fmt) = ref($data) =~ /.*::(.*)/;
if ($fmt eq 'fasta') {
$data = $data->file; # use the fasta file directly
}
else {
# convert
my $fh = File::Temp->new(TEMPLATE => 'DBDXXXXX',
UNLINK => 0,
DIR => $self->db_dir,
SUFFIX => '.fas');
my $fname = $fh->filename;
$fh->close;
$self->_register_temp_for_cleanup($fname);
my $fasio = Bio::SeqIO->new(-file=>">$fname", -format=>"fasta")
or $self->throw("Can't create temp fasta file");
require Bio::PrimarySeq;
if ($data->isa('Bio::AlignIO')) {
my $aln = $data->next_aln;
for ($aln->each_seq) {
# must de-gap
my $s = $_->seq;
my $a = $_->alphabet;
$s =~ s/[$Bio::PrimarySeq::GAP_SYMBOLS]//g;
$_->seq( $s );
$_->alphabet($a);
$fasio->write_seq($_)
}
}
elsif ($data->isa('Bio::SeqIO')) {
while (local $_ = $data->next_seq) {
my $s = $_->seq;
my $a = $_->alphabet;
$s =~ s/[$Bio::PrimarySeq::GAP_SYMBOLS]//g;
$_->seq( $s );
$_->alphabet($a);
$fasio->write_seq($_);
}
}
elsif ($data->isa('Bio::Align::AlignI')) {
for( $data->each_seq) {
my $s = $_->seq;
my $a = $_->alphabet;
$s =~ s/[$Bio::PrimarySeq::GAP_SYMBOLS]//g;
$_->seq( $s );
$_->alphabet($a);
$fasio->write_seq($_)
}
}
elsif ($data->isa('Bio::Seq') || $data->isa('Bio::PrimarySeq')) {
my $s = $data->seq;
my $a = $data->alphabet;
$s =~ s/[$Bio::PrimarySeq::GAP_SYMBOLS]//g;
$data->seq($s);
$data->alphabet($a);
$fasio->write_seq($data);
}
else {
$self->throw("Can't handle sequence container object ".
"of type '".ref($data)."'");
}
$fasio->close;
$data = $fname;
}
last;
};
}
return $data;
}
=head2 _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)
=cut
sub _register_temp_for_cleanup {
my $self = shift;
my @files = @_;
for (@files) {
my ($v, $d, $n) = File::Spec->splitpath($_);
$_ = File::Spec->catfile($self->db_dir, $n) unless length($d);
push @{$self->{_cleanup_list}}, File::Spec->rel2abs($_);
}
return 1;
}
=head2 cleanup()
Title : cleanup
Usage :
Function: unlink files registered for cleanup
Returns : true on success
Args :
=cut
sub cleanup {
my $self = shift;
return unless $self->{_cleanup_list};
for (@{$self->{_cleanup_list}}) {
m/(\.[a-z0-9_]+)+$/i && do {
unlink $_;
next;
};
do { # catch all index files
if ( -e $_.".psq" ) {
unlink glob($_.".p*");
unlink glob($_.".??.p*");
}
elsif ( -e $_.".nsq" ) {
unlink glob($_.".n*");
unlink glob($_.".??.n*");
}
else {
unlink $_;
}
next;
};
}
return 1;
}
=head2 AUTOLOAD
In this module, C<AUTOLOAD()> delegates L<Bio::Tools::Run::WrapperBase> and
L<Bio::Tools::Run::WrapperBase::CommandExts> methods (including those
of L<Bio::ParamterBaseI>) to the C<factory()> attribute:
$fac->stderr
gives you
$fac->factory->stderr
If $AUTOLOAD isn't pointing to a WrapperBase method, then AUTOLOAD attempts to return a C<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 C<run> with the C<-method> parameter appropriately set.
=cut
sub AUTOLOAD {
my $self = shift;
my @args = @_;
my $method = $AUTOLOAD;
$method =~ s/.*:://;
my @ret;
if (grep /^$method$/, @Bio::Tools::Run::StandAloneBlastPlus::BlastMethods) {
push @args, ('-method_args' => ['-remote' => 1] ) if ($self->is_remote);
return $self->run( -method => $method, @args );
}
if ($self->factory and $self->factory->can($method)) { # factory method
return $self->factory->$method(@args);
}
if ($self->db_info and grep /^$method$/, keys %{$self->db_info}) {
return $self->db_info->{$method};
}
# else, fail
$self->throw("Can't locate method '$method' in class ".ref($self));
}
1;