Bio::SearchIO::hmmer_pull.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

     # 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";
             }
         }
     }
 
 

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:
   http://bugzilla.open-bio.org/
 
 

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 = 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'.
 
 

next_result

  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
 
 

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