/ 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO

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.org/howtos/SearchIO_HOWTO.html

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    :

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    :

format

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)

_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    :