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