Bio::Matrix::PSM::PsmHeaderI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::PsmHeaderI(3pm)
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 $release
";
#Now let's see what are the consensus sequences of the motifs fed as an input:
my %seq=$psmIO->seq;
#let's cycle through all consensus sequences now:
foreach my $id ($psmIO->hid) {
print "Motif $id is ",$seq{$id},"
";
}
#Finally look at the stuff we do not parse:
my @inputfile=grep(/datafile/i,$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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Matrix::PSM::PsmHeaderI(3pm)