NAME

Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information

SYNOPSIS

  use Bio::LocatableSeq;
  use Bio::Seq::Meta::Array;

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

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

  $seq->meta('1 2 3 4 5 6 7 8 9 10');

  # or you could create the Meta object directly
  $seq = Bio::Seq::Meta::Array->new(-id=>'test',
                                    -seq=>'ACTGCTAGCT',
                                    -start=>2434,
                                    -start=>2443,
                                    -strand=>1,
                                    -meta=>'1 2 3 4 5 6 7 8 9 10',
                                    -verbose=>1, # to see warnings
                                   );


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

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 can be a string of variable length and can be a complex structure. Blank values are undef or zero.

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

This class can be used for storing sequence quality values but Bio::Seq::Quality has named methods that make it easier.

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.

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

meta_text

 Title   : meta_text
 Usage   : $meta_values  = $obj->meta_text($values_arrayref);
 Function: Variant of meta() guarantied to return a string
           representation  of meta data. For details, see L<meta>.
 Returns : a string
 Args    : new value, string or array ref, 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 : reference to an array of meta data
 Args    : scalar, name of the meta data set
           new value, string or array ref, 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, string or array ref, 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, string or array ref, 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, string or array ref, 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 (can be undef)
           new value, string or array ref, 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, string or array ref, 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

meta_length

 Title   : meta_length()
 Usage   : $meta_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    : -

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 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.