| Bio::Seq::MetaI(3pm) | User Contributed Perl Documentation | Bio::Seq::MetaI(3pm) |
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.
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]
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::Meta::Array, Bio::Seq::EncodedSeq, Bio::Tools::OddCodes, Bio::Seq::Quality
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.
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Please 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.
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:
https://github.com/bioperl/bioperl-live/issues
Email heikki-at-bioperl-dot-org
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 _
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 implementation. 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
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
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 : 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.
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 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, optional
integer, end position, optional
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 : integer, start position, optional
integer, end position, optional
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.
Returns : an array of names
Args : none
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
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
Title : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : -
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 : -
Implementing classes will need to rewrite these Bio::PrimaryI methods.
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
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.
| 2020-10-28 | perl v5.30.3 |