Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information # get a Bio::Seq::MetaI compliant object somehow # to test this is a meta seq object $obj->isa("Bio::Seq::MetaI") || $obj->throw("$obj not a Bio::Seq::MetaI"); # accessors $string = $obj->meta; $string = $obj->meta_text; $substring = $obj->submeta(12,50); $unique_key = $obj->accession_number(); This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, sequence quality data and nucleotide alignments with translations. The length of the meta data sequence is not dependent on the amount of the meta information. The meta information always covers all the residues, but a blank value is used to denote unavailable information. If necessary the implementation quietly truncates or extends meta information with blank values. Definition of blank is implementation dependent. Gaps in MSAs should not have meta information. At this point a residue in a sequence object can have only one meta value. If you need more, use multiple copies of the sequence object. Meta data storage can be implemented in various ways, e.g: string, array of scalars, array of hashes, array of objects. If the implementation so chooses, there can be more then one meta values associated to each residue. See named_meta and names_submeta. Note that use of arbitrary names is very prone to typos leading to creation of additional copies of meta data sets. Bio::Seq::Meta provides basic, pure perl implementation of sequences with meta information. See Bio::Seq::Meta. Application specific implementations will override and add to these methods.

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] Suffix _text guaranties that output is a string. Note that it does not limit the input. 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. 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. Bio::Seq::Meta, Bio::Seq::EncodedSeq, Bio::Tools::OddCodes, Bio::Seq::PrimaryQual, Bio::Seq::SeqWithQuality

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email heikki@ebi.ac.uk Chad Matsalla, bioinformatics@dieselwurks.com; Aaron Mackey, amackey@virginia.edu; Peter Schattner schattner@alum.mit.edu; Richard Adams, Richard.Adams@ed.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

meta
Title : meta Usage : $meta_values = $obj->meta($values_string); Function: Get and set method for the unnamed 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 implementation may choose to accept argument values in a string or in an array (reference) or in a hash (reference). The return value may be a string or an array reference, depending on the implentation. If in doubt, use meta_text() which is a variant guarantied to return a string. See L<meta_text>. The length of the returned value always matches the length of the sequence. Returns : A reference to an array or a string Args : new value, 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 the 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

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. If implementation tries to set values beyond the current sequence, they should be ignored. The return value may be a string or an array reference, depending on the implentation. 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, optional integer, end position, optional 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 : integer, start position, optional integer, end position, optional 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: Retrives 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 Implemeting classes will need to rewrite these Bio::PrimaryI 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::MetaI object Args : none

trunc
Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence Returns : a fresh Bio::Seq::MetaI implementing object Args : Two integers denoting first and last residue of the sub-sequence.