# $Id: MetaI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Seq::MetaI # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information =head1 SYNOPSIS # 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(); =head1 DESCRIPTION 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 L and L. 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 L. Application specific implementations will override and add to these methods. =head2 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] =over 3 =item _text Suffix B<_text> guaranties that output is a string. Note that it does not limit the input. =item sub Prefix B, 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. =item named_ Prefix 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 "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 L. =back =head1 SEE ALSO L, L, L, L, L =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org =head1 CONTRIBUTORS Chad Matsalla, bioinformatics@dieselwurks.com; Aaron Mackey, amackey@virginia.edu; Peter Schattner schattner@alum.mit.edu; Richard Adams, Richard.Adams@ed.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::MetaI; use strict; use base qw(Bio::Root::RootI); =head2 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. 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 =cut sub meta { shift->throw_not_implemented } =head2 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. Returns : a string Args : new value, optional =cut sub meta_text { shift->throw_not_implemented } =head2 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. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta { shift->throw_not_implemented } =head2 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. Returns : a string Args : scalar, name of the meta data set new value, optional =cut sub named_meta_text { shift->throw_not_implemented } =head2 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. Returns : A reference to an array or a string Args : integer, start position, optional integer, end position, optional new value, optional =cut sub submeta { shift->throw_not_implemented } =head2 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. Returns : a string Args : integer, start position, optional integer, end position, optional new value, optional =cut sub submeta_text { shift->throw_not_implemented } =head2 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. 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 =cut sub named_submeta { shift->throw_not_implemented } =head2 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. Returns : a string Args : scalar, name of the meta data Args : integer, start position, optional integer, end position, optional new value, optional =cut sub named_submeta_text { shift->throw_not_implemented } =head2 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 =cut sub meta_names { shift->throw_not_implemented } =head2 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 Returns : boolean 1 or 0 Args : optional boolean value =cut sub force_flush { shift->throw_not_implemented } =head2 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 =cut sub is_flush { shift->throw_not_implemented } =head2 meta_length Title : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : - =cut sub meta_length { shift->throw_not_implemented } =head2 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 : - =cut sub named_meta_length { shift->throw_not_implemented } =head1 Bio::PrimarySeqI methods Implemeting classes will need to rewrite these Bio::PrimaryI methods. =cut =head2 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 =cut sub revcom { shift->throw_not_implemented } =head2 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. =cut sub trunc { shift->throw_not_implemented } 1;