Christopher Fields > BioPerl-1.6.901 > Bio::SearchIO::hmmer

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

NAME ^

Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)

SYNOPSIS ^

    # do not use this class directly it is available through Bio::SearchIO
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer',
                               -file   => 't/data/L77119.hmmer');
    while( my $result = $in->next_result ) {
        # this is a Bio::Search::Result::HMMERResult 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 parser for HMMER output. It works with both HMMER2 and HMMER3

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 - Kai Blin ^

Email kai.blin-at-biotech.uni-tuebingen.de

APPENDIX ^

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

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