NAME¶
Bio::SearchIO::blast - Event generator for event based parsing of blast reports
SYNOPSIS¶
# Do not use this object directly - it is used as part of the
# Bio::SearchIO system.
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-format => 'blast',
-file => 't/data/ecolitst.bls');
while( my $result = $searchio->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
DESCRIPTION¶
This object encapsulated the necessary methods for generating events suitable
for building Bio::Search objects from a BLAST report file. Read the
Bio::SearchIO for more information about how to use this.
This driver can parse:
- •
- NCBI produced plain text BLAST reports from blastall, this also includes
PSIBLAST, PSITBLASTN, RPSBLAST, and bl2seq reports. NCBI XML BLAST output
is parsed with the blastxml SearchIO driver
- •
- WU-BLAST all reports
- •
- Jim Kent's BLAST-like output from his programs (BLASTZ, BLAT)
- •
- BLAST-like output from Paracel BTK output
bl2seq parsing¶
Since I cannot differentiate between BLASTX and TBLASTN since bl2seq doesn't
report the algorithm used - I assume it is BLASTX by default - you can supply
the program type with -report_type in the SearchIO constructor i.e.
my $parser = Bio::SearchIO->new(-format => 'blast',
-file => 'bl2seq.tblastn.report',
-report_type => 'tblastn');
This only really affects where the frame and strand information are put - they
will always be on the $hsp->query instead of on the $hsp->hit part of
the feature pair for blastx and tblastn bl2seq produced reports. Hope that's
clear...
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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich¶
Email Jason Stajich jason-at-bioperl.org
CONTRIBUTORS¶
Steve Chervitz sac-at-bioperl.org
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::SearchIO::blast->new(%args);
Function: Builds a new Bio::SearchIO::blast object
Returns : Bio::SearchIO::blast
Args : Key-value pairs:
-fh/-file => filehandle/filename to BLAST file
-format => 'blast'
-report_type => 'blastx', 'tblastn', etc -- only for bl2seq
reports when you want to distinguish between
tblastn and blastx reports (this only controls
where the frame information is put - on the query
or subject object.
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-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
-hit_filter => reference to a function to be used for
filtering hits based on arbitrary criteria.
All hits of each BLAST report must satisfy
this criteria to be retained.
If a hit fails this test, it is ignored.
This function should take a
Bio::Search::Hit::BlastHit.pm object as its first
argument and return true
if the hit should be retained.
Sample filter function:
-hit_filter => sub { $hit = shift;
$hit->gaps == 0; },
(Note: -filt_func is synonymous with -hit_filter)
-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.
The following criteria are not yet supported:
(these are probably best applied within this module rather than in the
event handler since they would permit the parser to take some shortcuts.)
-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.
next_result¶
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
_will_handle¶
Title : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
Args : string containing type of element.
Optimizations:
- 1.
- Using the cached pointer to the EventHandler to minimize repeated
lookups.
- 2.
- Caching the will_handle status for each type that is encountered so that
it only need be checked by calling handler->will_handle($type)
once.
This does not lead to a major savings by itself (only 5-10%). In combination
with other optimizations, or for large parse jobs, the savings good be
significant.
To test against the unoptimized version, remove the parentheses from around the
third term in the ternary " ? : " operator and add two calls to
$self->
_eventHandler().
start_element¶
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
end_element¶
Title : end_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : hashref with an element's worth of data
Args : hashref with at least 2 keys 'Data' and 'Name'
element¶
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convenience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
characters¶
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
within_element¶
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
See Also: in_element
in_element¶
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'within_element' because within
can be tested for a whole block.
Returns : boolean
Args : string element name
See Also: within_element
start_document¶
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
end_document¶
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
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 )
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.
signif¶
Synonym for
max_significance()
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.
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
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)
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)