NAME¶
Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA,
...)
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
}
}
}
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
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
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 & Steve Chervitz¶
Email jason-at-bioperl.org Email 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->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 Bio::Factory::ObjectFactoryI, 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.
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 :
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 :
Title : format
Usage : $format = $obj->format()
Function: Get the search format
Returns : search format
Args : none
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 Bio::SearchIO::EventHandlerI
_eventHandler¶
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::SearchIO::EventHandlerI
Args : none
See Bio::SearchIO::EventHandlerI
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 Bio::Root::RootI
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 Bio::Root::Exception
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 Bio::Root::Exception
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.
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
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 $obj->check_all_hits;
Purpose : Set/Get the indicator for whether or not to process all hits.
: If false, the parser will stop processing hits after the
: the first non-significance hit or the first hit that fails
: any hit filter.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
Title : _load_format_module
Usage : *INTERNAL SearchIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
_get_seq_identifiers¶
Title : _get_seq_identifiers
Usage : my ($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)
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :