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NAME

FAST::Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information

SYNOPSIS


            

              
              
use FAST::Bio::LocatableSeq;
use FAST::Bio::Seq::Meta;
use FAST::Bio::Tools::OddCodes;
use FAST::Bio::SeqIO;
my $seq = FAST::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 FAST::Bio::PrimarySeq, too
# to test this is a meta seq object
$seq->isa("FAST::Bio::Seq::Meta")
    || $seq->throw("$seq is not a FAST::Bio::Seq::Meta");
$seq->meta('1234567890');
$seq = FAST::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 FAST::Bio::Tools::OddCodes as meta data
my $protcodes = FAST::Bio::Tools::OddCodes->new(-seq => $seq);
my @codes = qw(structural chemical functional charge hydrophobic);
map { $seq->named_meta($_, ${$protcodes->$_($seq) } )} @codes;
my $out = FAST::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 FAST::Bio::LocatableSeq objects with additional methods to store that meta information. See FAST::Bio::LocatableSeq and FAST::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.

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

SEE ALSO

FAST::Bio::LocatableSeq, FAST::Bio::Seq::MetaI, FAST::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://redmine.open-bio.org/projects/bioperl/

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

FAST::Bio::PrimarySeqI methods

revcom


            

              
              
Title   : revcom
Usage   : $newseq = $seq->revcom();
Function: Produces a new FAST::Bio::Seq::MetaI implementing object where
          the order of residues and their meta information is reversed.
Returns : A new (fresh) FAST::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 FAST::Bio::Seq::Meta implementing object
Args    : Two integers denoting first and last residue of the sub-sequence.