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NAMEBio::Seq::Meta - Generic superclass for sequence objects with residue-based meta informationSYNOPSISuse Bio::LocatableSeq; use Bio::Seq::Meta; use Bio::Tools::OddCodes; use Bio::SeqIO; my $seq = 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 Bio::PrimarySeq, too # to test this is a meta seq object $seq->isa("Bio::Seq::Meta") || $seq->throw("$seq is not a Bio::Seq::Meta"); $seq->meta('1234567890'); $seq = 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 Bio::Tools::OddCodes as meta data my $protcodes = Bio::Tools::OddCodes->new(-seq => $seq); my @codes = qw(structural chemical functional charge hydrophobic); map { $seq->named_meta($_, ${$protcodes->$_($seq) } )} @codes; my $out = Bio::SeqIO->new(-format=>'metafasta'); $out->write_seq($seq); DESCRIPTIONThis 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 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. Bio::Seq::Meta::Array allows for more complex meta values (scalars or objects) to be used. Method namingCharacter 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]
NOTEThis 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.SEE ALSOBio::LocatableSeq, Bio::Seq::MetaI, Bio::Seq::Meta::ArrayFEEDBACKMailing ListsUser 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 SupportPlease 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 BugsReport 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 LehvaslaihoEmail heikki-at-bioperl-dot-orgCONTRIBUTORSChad Matsalla, bioinformatics@dieselwurks.comAaron Mackey, amackey@virginia.edu APPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _newTitle : 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 metaTitle : 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_textTitle : 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_metaTitle : 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_positionsTitle : _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_textTitle : 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 submetaTitle : 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_textTitle : 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_submetaTitle : 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_textTitle : 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_namesTitle : 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_lengthTitle : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : - named_meta_lengthTitle : 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_flushTitle : 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_flushTitle : _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_flushTitle : 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 methodsrevcomTitle : 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. truncTitle : 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.
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