[Bioperl-l] {SPECS] Sequence meta data
Heikki Lehvaslaiho
heikki at ebi.ac.uk
Mon Mar 31 11:28:56 EST 2003
I have put together a sequence class interface which tackles in
generic way storage of any kind of residue-based meta
information. There are already classes in BioPerl which work with
specific types of meta information, and more are likely to added, but
they do not work together.
The types of sequence meta data in question include:
Type Module or person
- sequence quality data Bio::Seq::PrimaryQual
- nucleotide alignments with translations Bio::Seq::EncodedSeq
- RNA secondary structure Peter Schattner
- protein secondary structure -
- protein hydrophobicity Bio::Tools::OddCodes
- other simplified amino acid alphabets Bio::Tools::OddCodes
...more?
I've written two modules: Bio::Seq::MetaI and a generic, pure perl
implementation Bio::Seq::Meta which can store and manipulate any meta
data encoding that uses exactly one character per residue.
The idea is that meta data makes sense only in the context of the
sequence and should be stored as an integral part of the sequence
object.
Fasta format should be easy extend to create a text format for
serialisation of this kind of data. E.g:
< myseq1
LIVHGGRPA
& myseq1
aaa bbbb
< myseq2
...
but I have not tried it out yet.
Bio::Seq::Meta name space should be preferably used to for more specific
implementations with more methods.
Please comment before I commit. POD docs more the modules are below
together with some tests.
-Heikki
------------------------------------------------------------------------
NAME
Bio::Seq::MetaI - Interface for sequence objects with residue-based
meta
information
SYNOPSIS
# 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();
DESCRIPTION
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 quality 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 metain formation 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.
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.
SEE ALSO
Bio::Seq::Meta, Bio::Seq::EncodedSeq, Bio::Tools::OddCodes,
Bio::Seq::PrimaryQual, Bio::Seq::SeqWithQuality
FEEDBACK
...
AUTHOR - Heikki Lehvaslaiho
Email heikki at ebi.ac.uk
CONTRIBUTORS
Chad Matsalla, bioinformatics at dieselwurks.com; Aaron Mackey,
amackey at virginia.edu
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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 implementation may choose to accept argument values
in
a string or in an array (reference) or in a hash
(reference).
Implementation should warn or throw an error if user
tries to set mata information to a gap character.
The return value may be a string or an array reference,
depending on the implentation. 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
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
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.
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 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, optional
submeta_text
Title : submeta_text
Usage : $meta_values = $obj->submeta_text(20, $value_string);
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
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::MetaI object
Args : none
trunc
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.
------------------------------------------------------------------------
NAME
Bio::Seq::MetaI - Generic superclass for sequence objects with
residue-based meta information
SYNOPSIS
# get a Bio::Seq::MetaI compliant object somehow, e.g.:
# use an existing sequence object
my $seq = Bio::LocatableSeq(-id=>'test',
-seq=>'ACTGCTAGCT',
-varbose=>1, # to see warnings
);
bless $seq, Bio::Seq::Meta;
# to test this is a meta seq object
$obj->isa("Bio::Seq::MetaI")
|| $obj->throw("$obj does not implement the Bio::Seq::MetaI
interface");
# accessors
$string = $obj->meta();
$substring = $obj->submeta(2,5);
$unique_key = $obj->accession_number();
# unique biological id
DESCRIPTION
This class implements generic methods for sequences with
residue-basedmeta 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 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 metainformation 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.
SEE ALSO
Bio::LocatableSeq
FEEDBACK
...
AUTHOR - Heikki Lehvaslaiho
Email heikki at ebi.ac.uk
CONTRIBUTORS
Chad Matsalla, bioinformatics at dieselwurks.com Aaron Mackey,
amackey at virginia.edu
APPENDIX
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 : meta data in a string
Args : new value, string, optional
_test_gap_positions
Title : _test_gap_positions
Usage : $meta_values = $obj->meta_text($values_arrayref);
Function: Internal test for correct position of gap characters.
Gap being only '-' this time.
This method is called from 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
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
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, optional
submeta_text
Title : submeta_text
Usage : $meta_values = $obj->submeta_text(20, $value_string);
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
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::MetaI 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::MetaI implementing object
Args : Two integers denoting first and last residue of the
sub-sequence.
------------------------------------------------------------------------
ok my $seq = Bio::Seq::Meta->new
( -seq => "",
-meta => "",
-alphabet => 'dna',
-id => 'no sequence and no quality but with an id'
);
# create a random sequence object
ok $seq = Bio::Seq::Meta->new( -seq => "AT-CGATCGA",
-id => 'test',
-verbose => 2
);
ok $seq->meta, " ";
# create some random meta values, but gap in the wrong place
my $metastring = "a-abb bb ";
eval {
$seq->meta($metastring);
};
ok 1 if $@ =~ 'column [2]';
$seq->verbose(1);
# create some random meta values, but not for the last residue
$metastring = "aa-bb bb";
ok $seq->meta($metastring), $metastring. " ";
# truncate the sequence by assignment
$seq->seq('AT-CGA');
$seq->alphabet('dna');
ok $seq->meta, 'aa-bb ';
ok $seq->meta_text, 'aa-bb ';
# truncate the sequence by trunc method
ok $seq->strand(-1), -1;
ok $seq = $seq->trunc(1,5);
ok $seq->seq, 'AT-CG';
ok $seq->meta, 'aa-bb';
ok $seq->strand, -1;
# revcom
ok $seq = $seq->revcom;
ok $seq->seq, 'CG-AT';
ok $seq->meta, 'bb-aa';
ok $seq->strand, 1;
# submeta
ok $seq->subseq(2,4), 'G-A';
ok $seq->submeta(2,4), 'b-a';
ok $seq->submeta(2,undef, 'c-c'), 'c-c';
ok $seq->submeta(2,4), 'c-c';
ok $seq->meta, 'bc-ca';
ok $seq->meta(''), ' ';
ok $seq->submeta(2,undef, 'c-c'), 'c-c';
ok $seq->meta, ' c-c ';
--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki at ebi.ac.uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________
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