NAME

FAST::Bio::SearchIO::blast_pull - A parser for BLAST 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 => 'blast_pull',
                           -file   => 't/data/new_blastn.txt');
while (my $result = $in->next_result) {
    # this is a FAST::Bio::Search::Result::BlastPullResult object
    print "Results for ", $result->query_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 BLAST output. It is fast since it only does work on request (hence 'pull').

Currently only NCBI BLASTN and BLASTP are supported.

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::blast_pull->new();
Function: Builds a new FAST::Bio::SearchIO::blast_pull object 
Returns : FAST::Bio::SearchIO::blast_pull
Args    : -fh/-file => BLAST output filename
          -format   => 'blast_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
          -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 'memory'.
            
          

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