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Manual Reference Pages  -  BIO::MATRIX::PSM::IO::MEME (3)

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NAME

Bio::Matrix::PSM::IO::meme - PSM meme parser implementation

CONTENTS

SYNOPSIS

See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers

DESCRIPTION

Parser for meme.

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Stefan Kirov

Email skirov@utk.edu

APPENDIX

    new



 Title   : new
 Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>meme,
                                                 -file=>$file);
 Function: Associates a file with the appropriate parser
 Throws  : Throws if the file passed is in HTML format or
           if the MEME header cannot be found.
 Example :
 Args    : hash
 Returns : "Bio::Matrix::PSM::$format"->new(@args);



    _parse_coordinates



 Title   : _parse_coordinates
 Usage   :
 Function:
 Throws  :
 Example : Internal stuff
 Returns :
 Args    :



    header



 Title   : header
 Usage   :  my %header=$psmIO->header;
 Function:  Returns the header for the MEME file
 Throws  :
 Example : Fetching all the sequences included in the MEME analysis,
           being parsed
           my %header=$psmIO->header;
            foreach my $seqid (@{$header{instances}}) {
               my $seq=$db->get_Seq_by_acc($id);
               #Do something with the sequence
            }
            where $db might be Bio::DB:GenBank object, see
 Returns : Hash with three keys: instances, weights and lengths, which
           should be self-explenatory. Each value is an array
           reference. Each array element corresponds to the same
           element in the other two arrays. So $header{instances}->[$i]
           will refer to the same sequence in the motif file as
           $header{weights}->[$i] and $header{lengths}->[$i]
 Args    :  none
 Notes   :  OBSOLETE!



    next_psm



 Title   : next_psm
 Usage   : my $psm=$psmIO->next_psm();
 Function: Reads the next PSM from the input file, associated with this object
 Throws  : Throws if the format is inconsistent with the rules for MEME 3.0.4:
            no SUMMARY Section present or some keywords are missing/altered.
 Example :
 Returns : Bio::Matrix::PSM::Psm object
 Args    : none



    _parseMatrix



 Title   : _parseMatrix
 Usage   :
 Function: Parses the next site matrix information in the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  hash as for constructing a SiteMatrix object (see SiteMatrixI)
 Args    :  string



    _parse_logs



 Title   : _parse_logs
 Usage   :
 Function: Parses the next site matrix log values in the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  array of array refs
 Args    :  string



    _parseInstance



 Title   : _parseInstance
 Usage   :
 Function:  Parses the next sites instances from the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  Bio::Matrix::PSM::InstanceSite object
 Args    :  none



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perl v5.20.3 BIO::MATRIX::PSM::IO::MEME (3) 2016-04-05

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