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


       Bio::SearchIO::hmmer_pull - A parser for HMMER output


           # do not use this class directly it is available through Bio::SearchIO
           use Bio::SearchIO;
           my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
                                      -file   => 't/data/hmmpfam.bigout');
           while (my $result = $in->next_result) {
               # this is a Bio::Search::Result::HmmpfamResult object
               print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
               while (my $hit = $result->next_hit) {
                   print $hit->name(), "\n";
                   while (my $hsp = $hit->next_hsp) {
                       print "length is ", $hsp->length(), "\n";


       This object implements a pull-parser for HMMER output. It is fast since it only does work
       on request (hence 'pull').


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AUTHOR - Sendu Bala



       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::hmmer_pull->new();
        Function: Builds a new Bio::SearchIO::hmmer_pull object
        Returns : Bio::SearchIO::hmmer_pull
        Args    : -fh/-file => HMMER output filename
                  -format   => 'hmmer_pull'
                  -evalue   => float or scientific notation number to be used
                               as an evalue cutoff for hits
                  -score    => integer or scientific notation number to be used
                               as a score value cutoff for hits
                  -hsps     => integer minimum number of hsps (domains) a hit must have
                  -piped_behaviour => 'temp_file'|'memory'|'sequential_read'

                  -piped_behaviour defines what the parser should do if the input is
                   an unseekable filehandle (eg. piped input), see
                   Bio::PullParserI::chunk for details. Default is 'sequential_read'.

        Title   : next_result
        Usage   : my $hit = $searchio->next_result;
        Function: Returns the next Result from a search
        Returns : Bio::Search::Result::ResultI object
        Args    : none

        Title   : result_count
        Usage   : my $count = $searchio->result_count
        Function: Returns the number of results we have processed.
        Returns : integer
        Args    : none

        Title   : rewind
        Usage   : $searchio->rewind;
        Function: Allow one to reset the Result iterator to the beginning, so that
                  next_result() will subsequently return the first result and so on.

                  NB: result objects are not cached, so you will get new result objects
                  each time you rewind. Also, note that result_count() counts the
                  number of times you have called next_result(), so will not be able
                  tell you how many results there were in the file if you use rewind().

        Returns : n/a
        Args    : none