Bio::Seq::Meta(3pm)

NAME
Bio::Seq::Meta - 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::Seq::Meta->new(-id=>'test',
                                   -seq=>'ACTGCTAGCT',
                                   -start=>2434,
                                   -end=>2443,
                                   -strand=>1,
                                   -verbose=>1, # to see warnings
                                  );

  # 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');
  $seq = Bio::Seq::Meta->new(-id=>'test',
                             -seq=>'HACILMIFGT',
                             -start=>2434,
                             -end=>2443,
                             -strand=>1,
                             -meta=>'1234567890',
                             -verbose=>1, # to see warnings
                            );

  # 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).

After the latest rewrite, the meta information no longer covers all the residues automatically. Methods to check the length of meta information (meta_length)and to see if the ends are flushed to the sequence have been added (is_flush). To force the old functionality, set force_flush to true.

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.

Bio::Seq::Meta::Array allows for more complex meta values (scalars or objects) to be used.

  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.

NOTE
This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq, which itself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so bless-ing objects of this class into a Bio::SeqI or vice versa and will not work as expected (see bug 2262). This may be addressed in a future refactor of Bio::LocatableSeq.

SEE ALSO
Bio::LocatableSeq, Bio::Seq::MetaI, Bio::Seq::Meta::Array

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

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, if force_flush() is set. See L<force_flush>.

 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.
 Returns : an array of names
 Args    : none

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

  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. Not done by default.
 Returns : boolean 1 or 0
 Args    : optional boolean value

Note that if you turn this forced padding off, the previously padded values are not changed.

  _do_flush
 Title   : _do_flush
 Usage   :
 Function: internal method to do the force that meta values are same
           length as the sequence . Called from L<force_flush>
 Returns :
 Args    :

  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

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
 Throws  : if the object returns false on is_flush()

Note: The method does nothing to meta values, it reorders them, only.

  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.