Provided by: libbio-perl-perl_1.7.6-3_all bug

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.