Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
use Bio::SearchIO; # format can be 'fasta', 'blast', 'exonerate', ... my $searchio = new Bio::SearchIO( -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 } } }
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 (NCBI not 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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::SearchIO(); 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.
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 : 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
Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::SearchIO::EventHandlerI Args : none
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
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
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.
Title : result_count Usage : $num = $stream->result_count; Function: Gets the number of Blast results that have been parsed. Returns : integer Args : none Throws : none
Title : _load_format_module Usage : *INTERNAL SearchIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.