Bio::Seq::MetaI(3pm)

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:

  https://github.com/bioperl/bioperl-live/issues

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 implementation. 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 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, 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: Retrieves 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
Implementing 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.