Bio::Matrix::PSM::PsmHeaderI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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