SYNOPSIS
use 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);
DESCRIPTION
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).
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 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]
- _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.
- sub
- 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.
- named
-
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.
NOTE
This 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.FEEDBACK
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-orgAPPENDIX
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, if force_flush() is set. See L<force_flush>.
Returns : meta data in a string
Args : new value, string, 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, 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 : a string
Args : scalar, name of the meta data set
new value, 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, 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 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_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, 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, 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, optional
meta_names
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
meta_length
Title : meta_length() Usage : $meeta_len = $obj->meta_length(); Function: return the number of elements in the meta set Returns : integer Args : -
named_meta_length
Title : 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_flush
Title : 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_flush
Title : _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_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
Bio::PrimarySeqI methods
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
Throws : if the object returns false on is_flush()
Note: The method does nothing to meta values, it reorders them, only.
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.