NAME

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

SYNOPSIS

# do not use this class directly it is available through FAST::Bio::SearchIO
use FAST::Bio::SearchIO;
my $in = FAST::Bio::SearchIO->new(-format => 'hmmer_pull',
                           -file   => 't/data/hmmpfam.bigout');
while (my $result = $in->next_result) {
    # this is a FAST::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";
        }
    }
}

DESCRIPTION

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

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

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 = FAST::Bio::SearchIO::hmmer_pull->new();
Function: Builds a new FAST::Bio::SearchIO::hmmer_pull object 
Returns : FAST::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
           FAST::Bio::PullParserI::chunk for details. Default is 'sequential_read'.

next_result

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

result_count

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

rewind

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