#
# BioPerl module for Bio::SearchIO
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO - Driver for parsing Sequence Database Searches
(BLAST, FASTA, ...)
=head1 SYNOPSIS
use Bio::SearchIO;
# format can be 'fasta', 'blast', 'exonerate', ...
my $searchio = Bio::SearchIO->new( -format => 'blastxml',
-file => 'blastout.xml' );
while ( my $result = $searchio->next_result() ) {
while( my $hit = $result->next_hit ) {
# process the Bio::Search::Hit::HitI object
while( my $hsp = $hit->next_hsp ) {
# process the Bio::Search::HSP::HSPI object
}
}
}
=head1 DESCRIPTION
This is a driver for instantiating a parser for report files from
sequence database searches. This object serves as a wrapper for the
format parsers in Bio::SearchIO::* - you should not need to ever
use those format parsers directly. (For people used to the SeqIO
system it, we are deliberately using the same pattern).
Once you get a SearchIO object, calling next_result() gives you back
a L<Bio::Search::Result::ResultI> compliant object, which is an object that
represents one Blast/Fasta/HMMER whatever report.
A list of module names and formats is below:
blast BLAST (WUBLAST, NCBIBLAST,bl2seq)
fasta FASTA -m9 and -m0
blasttable BLAST -m9 or -m8 output (both NCBI and WUBLAST tabular)
megablast MEGABLAST
psl UCSC PSL format
waba WABA output
axt AXT format
sim4 Sim4
hmmer HMMER2 hmmpfam and hmmsearch or HMMER3 hmmscan and hmmsearch
exonerate Exonerate CIGAR and VULGAR format
blastxml NCBI BLAST XML
wise Genewise -genesf format
Also see the SearchIO HOWTO:
http://bioperl.open-bio.org/wiki/HOWTO:SearchIO
=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:
I<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:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich & Steve Chervitz
Email jason-at-bioperl.org
Email sac-at-bioperl.org
=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::SearchIO;
use strict;
use warnings;
# Object preamble - inherits from Bio::Root::IO
use Bio::SearchIO::SearchResultEventBuilder;
# Special exception class for exceptions during parsing.
# End users should not ever see these.
# For an example of usage, see blast.pm.
@Bio::SearchIO::InternalParserError::ISA = qw(Bio::Root::Exception);
use Symbol;
use base qw(Bio::Root::IO Bio::Event::EventGeneratorI Bio::AnalysisParserI);
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO->new();
Function: Builds a new Bio::SearchIO object
Returns : Bio::SearchIO initialized with the correct format
Args : -file => $filename
-format => format
-fh => filehandle to attach to
-result_factory => object implementing Bio::Factory::ObjectFactoryI
-hit_factory => object implementing Bio::Factory::ObjectFactoryI
-hsp_factory => object implementing Bio::Factory::ObjectFactoryI
-writer => object implementing Bio::SearchIO::SearchWriterI
-output_format => output format, which will dynamically load writer
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-check_all_hits => boolean. Check all hits for significance against
significance criteria. Default = false.
If false, stops processing hits after the first
non-significant hit or the first hit that fails
the hit_filter call. This speeds parsing,
taking advantage of the fact that the hits are
processed in the order they appear in the report.
-min_query_len => integer to be used as a minimum for query sequence
length. Reports with query sequences below this
length will not be processed.
default = no minimum length.
-best => boolean. Only process the best hit of each report;
default = false.
See L<Bio::Factory::ObjectFactoryI>, L<Bio::SearchIO::SearchWriterI>
Any factory objects in the arguments are passed along to the
SearchResultEventBuilder object which holds these factories and sets
default ones if none are supplied as arguments.
=cut
# TODO: The below don't seem to be implemented (e.g. in Bio::SearchIO::blast)
#
# -score => integer or scientific notation number to be used
# as a blast score value cutoff
# -bits => integer or scientific notation number to be used
# as a bit score value cutoff
# -overlap => integer. The amount of overlap to permit between
# adjacent HSPs when tiling HSPs. A reasonable value is 2.
# default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP.
sub new {
my($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::SearchIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'blast';
my $output_format = $param{'-output_format'};
my $writer = undef;
if( defined $output_format ) {
if( defined $param{'-writer'} ) {
my $dummy = Bio::Root::Root->new();
$dummy->throw("Both writer and output format specified - not good");
}
if( $output_format =~ /^blast$/i ) {
$output_format = 'TextResultWriter';
}
my $output_module = "Bio::SearchIO::Writer::".$output_format;
$class->_load_module($output_module);
$writer = $output_module->new(@args);
push(@args,"-writer",$writer);
}
# normalize capitalization to lower case
$format = "\L$format";
return unless( $class->_load_format_module($format) );
return "Bio::SearchIO::${format}"->new(@args);
}
}
sub _initialize {
my($self, @args) = @_;
$self->{'_handler'} = undef;
# not really necessary unless we put more in RootI
#$self->SUPER::_initialize(@args);
# initialize the IO part
$self->_initialize_io(@args);
$self->attach_EventHandler(Bio::SearchIO::SearchResultEventBuilder->new(@args));
$self->{'_reporttype'} = '';
$self->{_notfirsttime} = 0;
my ($min_qlen, $check_all, $overlap, $best, $it, $writer ) =
$self->_rearrange([qw(
MIN_LENGTH
CHECK_ALL_HITS
OVERLAP
BEST
INCLUSION_THRESHOLD
WRITER)], @args); # note: $overlap isn't used for some reason
$writer && $self->writer( $writer );
defined $it && $self->inclusion_threshold($it);
defined $min_qlen && $self->min_query_length($min_qlen);
defined $best && $self->best_hit_only($best);
defined $check_all && $self->check_all_hits($check_all);
}
=head2 newFh
Title : newFh
Usage : $fh = Bio::SearchIO->newFh(-file=>$filename,
-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::SearchIO->newFh(-file=>$filename,
-format=>'Format')
$result = <$fh>; # read a ResultI object
print $fh $result; # write a ResultI object
Returns : filehandle tied to the Bio::SearchIO::Fh class
Args :
=cut
sub newFh {
my $class = shift;
return unless my $self = $class->new(@_);
return $self->fh;
}
=head2 fh
Title : fh
Usage : $obj->fh
Function:
Example : $fh = $obj->fh; # make a tied filehandle
$result = <$fh>; # read a ResultI object
print $fh $result; # write a ResultI object
Returns : filehandle tied to the Bio::SearchIO::Fh class
Args :
=cut
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
=head2 format
Title : format
Usage : $format = $obj->format()
Function: Get the search format
Returns : search format
Args : none
=cut
# format() method inherited from Bio::Root::IO
=head2 attach_EventHandler
Title : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::SearchIO::EventHandlerI
See L<Bio::SearchIO::EventHandlerI>
=cut
sub attach_EventHandler{
my ($self,$handler) = @_;
return if( ! $handler );
if( ! $handler->isa('Bio::SearchIO::EventHandlerI') ) {
$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::SearchIO::EventHandlerI');
}
$self->{'_handler'} = $handler;
return;
}
=head2 _eventHandler
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::SearchIO::EventHandlerI
Args : none
See L<Bio::SearchIO::EventHandlerI>
=cut
sub _eventHandler{
my ($self) = @_;
return $self->{'_handler'};
}
=head2 next_result
Title : next_result
Usage : $result = stream->next_result
Function: Reads the next ResultI object from the stream and returns it.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2) (see
Bio::Root::RootI POD page).
Returns : A Bio::Search::Result::ResultI object
Args : n/a
See L<Bio::Root::RootI>
=cut
sub next_result {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 write_result
Title : write_result
Usage : $stream->write_result($result_result, @other_args)
Function: Writes data from the $result_result object into the stream.
: Delegates to the to_string() method of the associated
: WriterI object.
Returns : 1 for success and 0 for error
Args : Bio::Search:Result::ResultI object,
: plus any other arguments for the Writer
Throws : Bio::Root::Exception if a Writer has not been set.
See L<Bio::Root::Exception>
=cut
sub write_result {
my ($self, $result, @args) = @_;
if( not ref($self->{'_result_writer'}) ) {
$self->throw("ResultWriter not defined.");
}
@args = $self->{'_notfirsttime'} unless( @args );
my $str = $self->writer->to_string( $result, @args);
$self->{'_notfirsttime'} = 1;
$self->_print( "$str" ) if defined $str;
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 write_report
Title : write_report
Usage : $stream->write_report(SearchIO stream, @other_args)
Function: Writes data directly from the SearchIO stream object into the
: writer. This is mainly useful if one has multiple ResultI objects
: in a SearchIO stream and you don't want to reiterate header/footer
: between each call.
Returns : 1 for success and 0 for error
Args : Bio::SearchIO stream object,
: plus any other arguments for the Writer
Throws : Bio::Root::Exception if a Writer has not been set.
See L<Bio::Root::Exception>
=cut
sub write_report {
my ($self, $result, @args) = @_;
if( not ref($self->{'_result_writer'}) ) {
$self->throw("ResultWriter not defined.");
}
@args = $self->{'_notfirsttime'} unless( @args );
my $str = $self->writer->to_string( $result, @args);
$self->{'_notfirsttime'} = 1;
$self->_print( "$str" ) if defined $str;
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 writer
Title : writer
Usage : $writer = $stream->writer;
Function: Sets/Gets a SearchWriterI object to be used for this searchIO.
Returns : 1 for success and 0 for error
Args : Bio::SearchIO::SearchWriterI object (when setting)
Throws : Bio::Root::Exception if a non-Bio::SearchIO::SearchWriterI object
is passed in.
=cut
sub writer {
my ($self, $writer) = @_;
if( ref($writer) and $writer->isa( 'Bio::SearchIO::SearchWriterI' )) {
$self->{'_result_writer'} = $writer;
}
elsif( defined $writer ) {
$self->throw("Can't set ResultWriter. Not a Bio::SearchIO::SearchWriterI: $writer");
}
return $self->{'_result_writer'};
}
=head2 result_count
Title : result_count
Usage : $num = $stream->result_count;
Function: Gets the number of Blast results that have been successfully parsed
at the point of the method call. This is not the total # of results
in the file.
Returns : integer
Args : none
Throws : none
=cut
sub result_count {
my $self = shift;
$self->throw_not_implemented;
}
=head2 inclusion_threshold
Title : inclusion_threshold
Usage : my $incl_thresh = $isreb->inclusion_threshold;
: $isreb->inclusion_threshold(1e-5);
Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
score matrix model (blastpgp) that was used for generating the reports
being parsed.
Returns : number (real)
Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
Args : number (real) (e.g., 0.0001 or 1e-4 )
=cut
# Delegates to the event handler.
sub inclusion_threshold {
shift->_eventHandler->inclusion_threshold(@_);
}
=head2 max_significance
Usage : $obj->max_significance();
Purpose : Set/Get the P or Expect value used as significance screening cutoff.
This is the value of the -signif parameter supplied to new().
Hits with P or E-value above this are skipped.
Returns : Scientific notation number with this format: 1.0e-05.
Argument : Scientific notation number or float (when setting)
Comments : Screening of significant hits uses the data provided on the
: description line. For NCBI BLAST1 and WU-BLAST, this data
: is P-value. for NCBI BLAST2 it is an Expect value.
=cut
sub max_significance { shift->{'_handler_cache'}->max_significance(@_) }
=head2 signif
Synonym for L<max_significance()|max_significance>
=cut
sub signif { shift->max_significance(@_) }
=head2 min_score
Usage : $obj->min_score();
Purpose : Set/Get the Blast score used as screening cutoff.
This is the value of the -score parameter supplied to new().
Hits with scores below this are skipped.
Returns : Integer or scientific notation number.
Argument : Integer or scientific notation number (when setting)
Comments : Screening of significant hits uses the data provided on the
: description line.
=cut
sub min_score { shift->{'_handler_cache'}->min_score(@_) }
=head2 min_query_length
Usage : $obj->min_query_length();
Purpose : Gets the query sequence length used as screening criteria.
This is the value of the -min_query_len parameter supplied to new().
Hits with sequence length below this are skipped.
Returns : Integer
Argument : n/a
=cut
sub min_query_length {
my $self = shift;
if (@_) {
my $min_qlen = shift;
if ( $min_qlen =~ /\D/ or $min_qlen <= 0 ) {
$self->throw(
-class => 'Bio::Root::BadParameter',
-text => "Invalid minimum query length value: $min_qlen\n"
. "Value must be an integer > 0. Value not set.",
-value => $min_qlen
);
}
$self->{'_confirm_qlength'} = 1;
$self->{'_min_query_length'} = $min_qlen;
}
return $self->{'_min_query_length'};
}
=head2 best_hit_only
Title : best_hit_only
Usage : print "only getting best hit.\n" if $obj->best_hit_only;
Purpose : Set/Get the indicator for whether or not to process only
: the best BlastHit.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
=cut
sub best_hit_only {
my $self = shift;
if (@_) { $self->{'_best'} = shift; }
$self->{'_best'};
}
=head2 check_all_hits
Title : check_all_hits
Usage : print "checking all hits.\n" if $obj->check_all_hits;
Purpose : Set/Get the indicator for whether or not to process all hits.
: If false, the parser will stop processing hits after the
: the first non-significance hit or the first hit that fails
: any hit filter.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
=cut
sub check_all_hits {
my $self = shift;
if (@_) { $self->{'_check_all'} = shift; }
$self->{'_check_all'};
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL SearchIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::SearchIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the SearchIO system please see the SearchIO docs.
This includes ways of checking for formats at compile time, not run time
END
;
}
return $ok;
}
=head2 _get_seq_identifiers
Title : _get_seq_identifiers
Usage : my ($gi, $acc,$ver) = &_get_seq_identifiers($id)
Function: Private function to get the gi, accession, version data
for an ID (if it is in NCBI format)
Returns : 3-pule of gi, accession, version
Args : ID string to process (NCBI format)
=cut
sub _get_seq_identifiers {
my ($self, $id) = @_;
return unless defined $id;
my ($gi, $acc, $version );
if ( $id =~ /^gi\|(\d+)\|/ ) {
$gi = $1;
}
if ( $id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|(.*)/ ) {
( $acc, $version ) = split /\./, $2;
}
elsif ( $id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/ ) {
( $acc, $version ) = split /\./, $3;
}
else {
#punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
#Database Name Identifier Syntax
#============================ ========================
#GenBank gb|accession|locus
#EMBL Data Library emb|accession|locus
#DDBJ, DNA Database of Japan dbj|accession|locus
#NBRF PIR pir||entry
#Protein Research Foundation prf||name
#SWISS-PROT sp|accession|entry name
#Brookhaven Protein Data Bank pdb|entry|chain
#Patents pat|country|number
#GenInfo Backbone Id bbs|number
#General database identifier gnl|database|identifier
#NCBI Reference Sequence ref|accession|locus
#Local Sequence identifier lcl|identifier
$acc = $id;
}
return ($gi, $acc, $version );
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'blast' if (/\.(blast|t?bl\w)$/i );
return 'fasta' if (/\.
(?: t? fas (?:ta)? |
m\d+ |
(?: t? (?: fa | fx | fy | ff | fs ) ) |
(?: (?:ss | os | ps) (?:earch)? ))
$/ix );
return 'blastxml' if ( /\.(blast)?xml$/i);
return 'exonerate' if ( /\.exon(erate)?/i );
}
sub close {
my $self = shift;
if( $self->writer ) {
$self->_print($self->writer->end_report());
$self->{'_result_writer'}= undef;
}
$self->SUPER::close(@_);
}
sub DESTROY {
my $self = shift;
$self->close() if defined $self->_fh;
$self->SUPER::DESTROY;
}
sub TIEHANDLE {
my $class = shift;
return bless {processor => shift}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'processor'}->next_result() || undef unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'processor'}->next_result();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'processor'}->write_result(@_);
}
1;
__END__