Bio::Seq::MetaI - Generic superclass for sequence objects with residue-based meta information
use Bio::LocatableSeq; use Bio::Seq::Meta; use Bio::Tools::OddCodes; use Bio::SeqIO; my $seq = Bio::LocatableSeq->new(-id=>'test', -seq=>'ACTGCTAGCT', -start=>2434, -start=>2443, -strand=>1, -verbose=>1, # to see warnings ); bless $seq, Bio::Seq::Meta; # 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'); # 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);
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 is always one character per residue long and blank values are space characters (ASCII 32).
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. If necessary, the implementation quietly truncates or extends meta information with blank values.
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.
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.
In this implementation, the output is always text, so these methods are redundant.
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::LocatableSeq
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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. Returns : meta data in a string Args : new value, string, optional
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, optional
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
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 : 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
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 if it contains any data. Returns : an array of names Args : none
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
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.