NAME

Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file

SYNOPSIS

 use Bio::Matrix::PSM::IO;
 #Obtain an Bio::Matrix::PSM::IO object:
 my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast');

 #Get some general data about the file you are parsing:
 my $release=$psmIO->release;
 my $version=$psmIO->version;

 print "This analysis was performed using MAST version $version, release $release\n";

 #Now let's see what are the consensus sequences of the motifs fed as an input:
 my %seq=$psmIO->seq;

 #let's cycle through all consensus sequences now:

 foreach my $id ($psmIO->hid) {
   print "Motif $id is \t",$seq{$id},"\n";
 }

  #Finally look at the stuff we do not parse:
  my @inputfile=grep(/datafile/i,$psmIO->unstructured);

DESCRIPTION

Generally you should not use this object directly, you can access the information through a PSM driver (See Bio::Matrix::PSM::IO). It is handling the header data from a PSM file which may be very different. This means that some of the methods will return undef naturally, because this information is not present in the file which is parsed. Some important data might be left over in the unstructured part, and you might have to parse it yourself. I will try to 'structure' this header more in the near future.

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 $header= Bio::Matrix::PSM::PsmHeader->new
            ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
              -instances=>\%instances, -header=>\@header, -type=>'mast');
 Function: Creates a new Bio::Matrix::PSM::PsmHeader object
 Throws  :
 Example :
 Returns :  Bio::Matrix::PSM::PsmHeaderI object
 Args    :  hash

seq

 Title   : seq
 Usage   : my %seq= $header->seq();
 Function: Returns the sequence data as a hash, indexed by a 
           sequence ID (motif id or accession number)
           In case the input data is a motif it would return the 
           consenus seq for each of them (mast).
 Throws  :
 Example :
 Returns :  hash
 Args    :

hid

 Title   : hid
 Usage   : my @ids= $header->hid();
 Function: Returns array with the motif/instance ids
 Throws  :
 Example :
 Returns :  array
 Args    :

length

 Title   : length
 Usage   : my %length= $header->length();
 Function: Returns the length of the input sequence or motifs as a hash, indexed
           by a sequence ID (motif id or accession number)
 Throws  :
 Example :
 Returns :  hash
 Args    :

instances

 Title   : instances
 Usage   : my %instances= $header->length();
 Function: Returns the instance, used  as a hash, indexed
           by a sequence ID (motif id or accession number)
 Throws  :
 Example :
 Returns :  hash of Bio::Matrix::PSM::InstanceSite objects
 Args    :

weights

 Title   : weights
 Usage   : my %weights= $header->weights();
 Function: Returns the weights of the input sequence as a hash, indexed
           by a sequence ID
 Throws  :
 Example :
 Returns :  hash
 Args    :

unstuctured

 Title   : unstuctured
 Usage   : my @unstructured= $header->unstuctured();
 Function: Returns the unstructured data in the header as an array, one line per
           array element, all control symbols are removed with \W
 Throws  :
 Example :
 Returns :   array
 Args    :

version

 Title   : version
 Usage   : my $version= $header->version;
 Function: Returns the version of the file being parsed if such exists
 Throws  :
 Example :
 Returns :  string
 Args    :

revision

 Title   : revision
 Usage   : my $revision= $header->revision;
 Function: Returns the revision of the file being parsed if such exists
 Throws  :
 Example :
 Returns :  string
 Args    :

_check

 Title   : _check
 Usage   : if ($self->_check('weights') { #do something} else {return 0;}
 Function: Checks if the method called is aplicable to the file format
 Throws  :
 Example :
 Returns :  boolean
 Args    :  string