Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN


           # generally we use Bio::SearchIO to build these objects
           use Bio::SearchIO;
           my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                                                  -file   => 'result.blast');

           while (my $result = $in->next_result) {
                       print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";


       This object implements a parser for NCBI BLASTN result output.


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AUTHOR - Sendu Bala



       Additional contributors names and emails here


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::SearchIO::Result::hmmpfam->new();
        Function: Builds a new Bio::SearchIO::Result::hmmpfam object
        Returns : Bio::SearchIO::Result::hmmpfam
        Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
                  -parent => Bio::PullParserI object (required if no -chunk)
                  -parameters => hash ref of search parameters (key => value), optional
                  -statistics => hash ref of search statistics (key => value), optional

                          where the array ref provided to -chunk contains an IO object
                  for a filehandle to something representing the raw data of the
                  result, and $start and $end define the tell() position within the
                  filehandle that the result data starts and ends (optional; defaults
                  to start and end of the entire thing described by the filehandle)

        Title   : next_hit
        Usage   : while( $hit = $result->next_hit()) { ... }
        Function: Returns the next available Hit object, representing potential
                  matches between the query and various entities from the database.
        Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
        Args    : none

        Title   : hits
        Usage   : my @hits = $result->hits
        Function: Returns the HitI objects contained within this Result
        Returns : Array of Bio::Search::Hit::HitI objects
        Args    : none

       See Also: Bio::Search::Hit::HitI

        Title          : sort_hits
        Usage          : $result->sort_hits('<score')
        Function       : Sorts the hits so that they come out in the desired order when
                     hits() or next_hit() is called.
        Returns        : n/a
        Args           : A coderef for the sort function. See the documentation on the Perl
                     sort() function for guidelines on writing sort functions.
                                 By default the sort order is ascending significance value (ie.
                                 most significant hits first).
                                 *** example

        Title   : rewind
        Usage   : $result->rewind;
        Function: Allow one to reset the Hit iterator to the beginning, so that
                  next_hit() will subsequently return the first hit and so on.
        Returns : n/a
        Args    : none

        Title   : get_statistic
        Usage   : my $gap_ext = $result->get_statistic('kappa')
        Function: Returns the value for a specific statistic available
                  from this result
        Returns : string
        Args    : name of statistic (string)

        Title   : get_parameter
        Usage   : my $gap_ext = $result->get_parameter('gapext')
        Function: Returns the value for a specific parameter used
                  when running this result
        Returns : string
        Args    : name of parameter (string)