Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information use Bio::LocatableSeq; use Bio::Seq::Meta::Array; my $seq = Bio::LocatableSeq->new(-id=>'test', -seq=>'ACTGCTAGCT', -start=>2434, -start=>2443, -strand=>1, -varbose=>1, # to see warnings ); bless $seq, Bio::Seq::Meta::Array; # the existing sequence object can be a Bio::PrimarySeq, too # to test this is a meta seq object $seq->isa("Bio::Seq::Meta::Array") || $seq->throw("$seq is not a Bio::Seq::Meta::Array"); $seq->meta('1 2 3 4 5 6 7 8 9 10'); # accessors $arrayref = $seq->meta(); $string = $seq->meta_text(); $substring = $seq->submeta_text(2,5); $unique_key = $seq->accession_number(); This 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 can be a string of variable length and can be a complex structure. Blank values are undef or zero. Application specific implementations should inherit from this class to override and add to these methods. Bio::LocatableSeq, Bio::Seq::MetaI, Bio::Seq::Meta,

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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 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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

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. Returns : reference to an array of meta data Args : new value, string or array ref, 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, string or array ref, 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 : reference to an array of meta data Args : scalar, name of the meta data set new value, string or array ref, 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, string or array ref, 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 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 integer, end position, optional when a third argument present new value, string or array ref, 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, string or array ref, 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, string or array ref, 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, string or array ref, 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 if it contains any data. Returns : an array of names Args : none

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::Meta object Args : none

trunc
Title : 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.