Bio::SearchIO(3) User Contributed Perl Documentation Bio::SearchIO(3)NAMEBio::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 HMMER hmmpfam 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:
http://bugzilla.open-bio.org/
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
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 :
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 :
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 = $stream->result_count;
Function: Gets the number of Blast results that have been successfully parsed
at the point of the method call. This is not the total # of results
in the file.
Returns : integer
Args : none
Throws : none
_load_format_module
Title : _load_format_module
Usage : *INTERNAL SearchIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
_get_seq_identifiers
Title : _get_seq_identifiers
Usage : my ($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)
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
perl v5.14.1 2011-07-22 Bio::SearchIO(3)
