/ 
bioperl-1.4
/ Bio::Seq::Meta

NAME

Bio::Seq::MetaI - Generic superclass for sequence objects with residue-based meta information

SYNOPSIS

use Bio::LocatableSeq;
use Bio::Seq::Meta;
use Bio::Tools::OddCodes;
use Bio::SeqIO;

my $seq = Bio::LocatableSeq->new(-id=>'test',
                                 -seq=>'ACTGCTAGCT',
                                 -start=>2434,
                                 -start=>2443,
                                 -strand=>1,
                                 -verbose=>1, # to see warnings
                                );

bless $seq, Bio::Seq::Meta;
# the existing sequence object can be a Bio::PrimarySeq, too

# to test this is a meta seq object
$seq->isa("Bio::Seq::Meta")
    || $seq->throw("$seq is not a Bio::Seq::Meta");

$seq->meta('1234567890');

# accessors

$string     = $seq->meta_text();
$substring  = $seq->submeta_text(2,5);
$unique_key = $seq->accession_number();

# storing output from Bio::Tools::OddCodes as meta data
my $protcodes = Bio::Tools::OddCodes->new(-seq => $seq);
my @codes = qw(structural chemical functional charge hydrophobic);
map { $seq->named_meta($_, ${$protcodes->$_($seq) } )} @codes;

my $out = Bio::SeqIO->new(-format=>'metafasta');
$out->write_seq($seq);

DESCRIPTION

This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See Bio::LocatableSeq and Bio::Seq::MetaI.

The meta information in this class is always one character per residue long and blank values are space characters (ASCII 32).

The length of the meta data sequence is not dependent on the amount of the meta information. The meta information always covers all the residues. If necessary, the implementation quietly truncates or extends meta information with blank values.

It is assumed that meta data values do not depend on the nucleotide sequence strand value.

Application specific implementations should inherit from this class to override and add to these methods.

Method naming

Character based meta data is read and set by method meta() and its variants. These are the suffixes and prefixes used in the variants:

[named_] [sub] meta [_text]
_text

Suffix _text guaranties that output is a string. Note that it does not limit the input.

In this implementation, the output is always text, so these methods are redundant.

sub

Prefix sub, like in subseq(), means that the method applies to sub region of the sequence range and takes start and end as arguments. Unlike subseq(), these methods are able to set values. If the range is not defined, it defaults to the complete sequence.

named_

Prefix named_ in method names allows the used to attach multiple meta strings to one sequence by explicitly naming them. The name is always the first argument to the method. The "unnamed" methods use the class wide default name for the meta data and are thus special cases "named" methods.

Note that internally names are keys in a hash and any misspelling of a name will silently store the data under a wrong name. The used names (keys) can be retrieved using method meta_names(). See meta_names.

SEE ALSO

Bio::LocatableSeq

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://bio.perl.org/MailList.html          - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho

Email heikki@ebi.ac.uk

CONTRIBUTORS

Chad Matsalla, bioinformatics@dieselwurks.com Aaron Mackey, amackey@virginia.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $metaseq = Bio::Seq::Meta->new
	        ( -meta => 'aaaaaaaabbbbbbbb',
                  -seq =>  'TKLMILVSHIVILSRM'
	          -id  => 'human_id',
	          -accession_number => 'S000012',
	        );
 Function: Constructor for Bio::Seq::Meta class, meta data being in a
           string. Note that you can provide an empty quality string.
 Returns : a new Bio::Seq::Meta object

meta

Title   : meta
Usage   : $meta_values  = $obj->meta($values_string);
Function:

          Get and set method for the meta data starting from residue
          position one. Since it is dependent on the length of the
          sequence, it needs to be manipulated after the sequence.

          The length of the returned value always matches the length
          of the sequence.

Returns : meta data in a string
Args    : new value, string, optional

meta_text

Title   : meta_text
Usage   : $meta_values  = $obj->meta_text($values_arrayref);
Function: Variant of meta() guarantied to return a textual
          representation  of meta data. For details, see L<meta>.
Returns : a string
Args    : new value, optional

named_meta

Title   : named_meta()
Usage   : $meta_values  = $obj->named_meta($name, $values_arrayref);
Function: A more general version of meta(). Each meta data set needs
          to be named. See also L<meta_names>.
Returns : a string
Args    : scalar, name of the meta data set
          new value, optional

_test_gap_positions

Title   : _test_gap_positions
Usage   : $meta_values  = $obj->_test_gap_positions($name);
Function: Internal test for correct position of gap characters.
          Gap being only '-' this time.

          This method is called from named_meta() when setting meta
          data but only if verbose is positive as this can be an
          expensive process on very long sequences. Set verbose(1) to
          see warnings when gaps do not align in sequence and meta
          data and turn them into errors by setting verbose(2).

Returns : true on success, prints warnings
Args    : none

named_meta_text

Title   : named_meta_text()
Usage   : $meta_values  = $obj->named_meta_text($name, $values_arrayref);
Function: Variant of named_meta() guarantied to return a textual
          representation  of the named meta data.
          For details, see L<meta>.
Returns : a string
Args    : scalar, name of the meta data set
          new value, optional

submeta

Title   : submeta
Usage   : $subset_of_meta_values = $obj->submeta(10, 20, $value_string);
          $subset_of_meta_values = $obj->submeta(10, undef, $value_string);
Function:

          Get and set method for meta data for subsequences.

          Numbering starts from 1 and the number is inclusive, ie 1-2
          are the first two residue of the sequence. Start cannot be
          larger than end but can be equal.

          If the second argument is missing the returned values
          should extend to the end of the sequence.

          The return value may be a string or an array reference,
          depending on the implementation. If in doubt, use
          submeta_text() which is a variant guarantied to return a
          string.  See L<submeta_text>.

Returns : A reference to an array or a string
Args    : integer, start position
          integer, end position, optional when a third argument present
          new value, optional

submeta_text

Title   : submeta_text
Usage   : $meta_values  = $obj->submeta_text(20, $value_string);
Function: Variant of submeta() guarantied to return a textual 
          representation  of meta data. For details, see L<meta>.
Returns : a string
Args    : new value, optional

named_submeta

Title   : named_submeta
Usage   : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string);
          $subset_of_meta_values = $obj->named_submeta($name, 10);
Function: Variant of submeta() guarantied to return a textual
          representation  of meta data. For details, see L<meta>.
Returns : A reference to an array or a string
Args    : scalar, name of the meta data set
          integer, start position
          integer, end position, optional when a third argument present
          new value, optional

named_submeta_text

Title   : named_submeta_text
Usage   : $meta_values  = $obj->named_submeta_text($name, 20, $value_string);
Function: Variant of submeta() guarantied to return a textual
          representation  of meta data. For details, see L<meta>.
Returns : a string
Args    : scalar, name of the meta data
Args    : integer, start position, optional
          integer, end position, optional
          new value, optional

meta_names

Title   : meta_names
Usage   : @meta_names  = $obj->meta_names()
Function: Retrieves an array of meta data set names. The default
          (unnamed) set name is guarantied to be the first name if it
          contains any data.
Returns : an array of names
Args    : none

Bio::PrimarySeqI methods

revcom

Title   : revcom
Usage   : $newseq = $seq->revcom();
Function: Produces a new Bio::Seq::MetaI implementing object where
          the order of residues and their meta information is reversed.
Returns : A new (fresh) Bio::Seq::Meta object
Args    : none

trunc

Title   : trunc
Usage   : $subseq = $seq->trunc(10,100);
Function: Provides a truncation of a sequence together with meta data
Returns : a fresh Bio::Seq::Meta implementing object
Args    : Two integers denoting first and last residue of the sub-sequence.