/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Matrix::PSM::IO::meme

NAME

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

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    :
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