Suffix <B>_textB> 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 <B>subB>, 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.|
Prefix <B>named_B> 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
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.
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.
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.
Please direct usage questions or support issues to the mailing list:
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.
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:
Chad Matsalla, firstname.lastname@example.org
Aaron Mackey, email@example.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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
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
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
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
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.
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 :
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
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.
|perl v5.20.3||BIO::SEQ::META (3)||2016-04-05|