Bio::Seq::MetaI.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   # get a Bio::Seq::MetaI compliant object somehow
 
   # to test this is a meta seq object
   $obj->isa("Bio::Seq::MetaI")
      || $obj->throw("$obj not a Bio::Seq::MetaI");
 
   # accessors
   $string     = $obj->meta;
   $string     = $obj->meta_text;
   $substring  = $obj->submeta(12,50);
   $unique_key = $obj->accession_number();
 
 

DESCRIPTION

This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, sequence quality data and nucleotide alignments with translations.

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, but a blank value is used to denote unavailable information. If necessary the implementation quietly truncates or extends meta information with blank values. Definition of blank is implementation dependent. Gaps in MSAs should not have meta information.

At this point a residue in a sequence object can have only one meta value. If you need more, use multiple copies of the sequence object.

Meta data storage can be implemented in various ways, e.g: string, array of scalars, array of hashes, array of objects.

If the implementation so chooses, there can be more then one meta values associated to each residue. See named_meta and names_submeta. Note that use of arbitrary names is very prone to typos leading to creation of additional copies of meta data sets.

Bio::Seq::Meta provides basic, pure perl implementation of sequences with meta information. See Bio::Seq::Meta. Application specific implementations will 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.
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::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::EncodedSeq, Bio::Tools::OddCodes, Bio::Seq::Quality

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 - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

CONTRIBUTORS

Chad Matsalla, bioinformatics@dieselwurks.com; Aaron Mackey, amackey@virginia.edu; Peter Schattner schattner@alum.mit.edu; Richard Adams, Richard.Adams@ed.ac.uk

APPENDIX

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

meta

  Title   : meta
  Usage   : $meta_values  = $obj->meta($values_string);
  Function:
 
            Get and set method for the unnamed 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 implementation may choose to accept argument values in
            a string or in an array (reference) or in a hash
            (reference).
 
            The return value may be a string or an array reference,
            depending on the implentation. If in doubt, use meta_text()
            which is a variant guarantied to return a string.  See
            L<meta_text>.
 
            The length of the returned value always matches the length
            of the sequence.
 
  Returns : A reference to an array or a string
  Args    : new value, 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 the 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
 
 

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.
 
            If implementation tries to set values beyond the current
            sequence, they should be ignored.
 
            The return value may be a string or an array reference,
            depending on the implentation. 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, optional
            integer, end position, optional
            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    : integer, start position, optional
            integer, end position, optional
            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: Retrives an array of meta data set names. The default (unnamed)
            set name is guarantied to be the first name.
  Returns : an array of names
  Args    : none
 
 

force_flush

  Title   : force_flush()
  Usage   : $force_flush = $obj->force_flush(1);
  Function: Automatically pad with empty values or truncate meta values to
             sequence length
  Returns : boolean 1 or 0
  Args    : optional boolean value
 
 

is_flush

  Title   : is_flush
  Usage   : $is_flush  = $obj->is_flush()
            or  $is_flush = $obj->is_flush($my_meta_name)
  Function: Boolean to tell if all meta values are in
            flush with the sequence length.
            Returns true if force_flush() is set
            Set verbosity to a positive value to see failed meta sets
  Returns : boolean 1 or 0
  Args    : optional name of the meta set
 
 

meta_length

  Title   : meta_length()
  Usage   : $meeta_len  = $obj->meta_length();
  Function: return the number of elements in the meta set
  Returns : integer
  Args    : -
 
 

named_meta_length

  Title   : named_meta_length()
  Usage   : $meeta_len  = $obj->named_meta_length($name);
  Function: return the number of elements in the named meta set
  Returns : integer
  Args    : -
 
 

Bio::PrimarySeqI methods

Implemeting classes will need to rewrite these Bio::PrimaryI 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::MetaI object
  Args    : none
 
 

trunc

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