Bio::Seq::Meta
Array
Summary
Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
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();
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 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.
Methods
Methods description
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 : reference to an array of meta data
Args : new value, string or array ref, 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 meta.
Returns : a string
Args : new value, string or array ref, 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 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 |
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 meta.
Returns : a string
Args : scalar, name of the meta data set
new value, string or array ref, 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 implentation. If in doubt, use
submeta_text() which is a variant guarantied to return a
string. See 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 |
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 meta.
Returns : a string
Args : new value, string or array ref, 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 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 |
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 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 |
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 |
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. |
Methods code
BEGIN {
$DEFAULT_NAME = 'DEFAULT';
$GAP = '-';
$META_GAP = 0;} | sub new
{ my ($class, %args) = @_;
if (defined($args{'-baseclass'})) {
@ISA = ($args{'-baseclass'},"Bio::Seq::MetaI");
}
else {
@ISA = qw( Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI );
}
my $self = $class->SUPER::new(%args);
my($meta) =
$self->_rearrange([qw(META
)],
%args);
$self->{'_meta'}->{$DEFAULT_NAME} = undef;
$meta && $self->meta($meta);
return $self; } | sub meta
{ shift->named_meta($DEFAULT_NAME, shift); } | sub meta_text
{ return join ' ', @{shift->meta(shift)};} | sub named_meta
{ my ($self, $name, $value) = @_;
$name ||= $DEFAULT_NAME;
if (defined $value) {
my ($arrayref);
if (ref $value eq 'ARRAY' ) {
$arrayref = $value;
}
elsif (not ref($value)) {
$arrayref = [split /\s+/, $value];
} else {
$self->throw("I need a scalar or array ref, not [". ref($value). "]");
}
my $diff = $self->length - @{$arrayref};
if ($diff > 0) {
foreach (1..$diff) { push @{$arrayref}, 0;}
}
$self->{'_meta'}->{$name} = $arrayref;
}
if (defined $self->{'_meta'}->{$name} and
scalar @{$self->{'_meta'}->{$name}} > $self->length ) {
return [@{$self->{'_meta'}->{$name}}[0..($self->length-1)]];
} else {
return $self->{'_meta'}->{$name} || (" " x $self->length);
}} | sub _test_gap_positions
{ my $self = shift;
my $name = shift;
my $success = 1;
$self->seq || return $success;
my $len = CORE::length($self->seq);
for (my $i=0; $i < $len; $i++) {
my $s = substr $self->{seq}, $i, 1;
my $m = substr $self->{_meta}->{$name}, $i, 1;
$self->warn("Gap mismatch in column [". ($i+1). "] of [$name] meta data in seq [". $self->id. "]")
and $success = 0
if ($m eq '-') && $s ne $m;
}
return $success;} | sub named_meta_text
{ return join ' ', @{shift->named_meta(@_)};} | sub submeta
{ shift->named_submeta($DEFAULT_NAME, @_); } | sub submeta_text
{ return join ' ', @{shift->submeta(@_)};} | sub named_submeta
{ my ($self, $name, $start, $end, $value) = @_;
$name ||= $DEFAULT_NAME;
$start ||=1;
$start =~ /^[+]?\d+$/ and $start > 0 or
$self->throw("Need at least a positive integer start value");
$start--;
my $metaref = $self->{_meta}->{$name};
if (defined $value) {
my $arrayref;
$self->warn("You are setting meta values beyond the length of the sequence\n".
"[$start > ". length($self->seq)."] in sequence ". $self->id)
if $start > $self->length;
if (ref $value eq 'ARRAY' ) {
$arrayref = $value;
}
elsif (not ref($value)) {
$arrayref = [split /\s+/, $value];
} else {
$self->throw("I need a scalar or array ref, not [". ref($value). "]");
}
$end or $end = @{$arrayref} + $start;
$end--;
my $diff = $end - $start - scalar @{$arrayref};
if ($diff > 0) {
foreach (1..$diff) { push @{$arrayref}, $META_GAP}
}
@{$metaref}[$start..$end] = @{$arrayref};
return $arrayref;
} else {
$end or $end = $self->length;
$end = $self->length if $end > $self->length;
$end--;
return [@{$metaref}[$start..$end]];
}} | sub named_submeta_text
{ return join ' ', @{shift->named_submeta(@_)};} | sub meta_names
{ my ($self) = @_;
my @r;
foreach ( sort keys %{$self->{'_meta'}} ) {
push (@r, $_) unless $_ eq $DEFAULT_NAME;
}
unshift @r, $DEFAULT_NAME if $self->{'_meta'}->{$DEFAULT_NAME};
return @r;} | sub revcom
{ my $self = shift;
my $new = $self->SUPER::revcom;
my $end = $self->length - 1;
map {
$new->{_meta}->{$_} = [ reverse @{$self->{_meta}->{$_}}[0..$end]]
} keys %{$self->{_meta}};
return $new;} | sub trunc
{ my ($self, $start, $end) = @_;
$start =~ /^[+]?\d+$/ and $start > 0 or
$self->throw("Need at least a positive integer start value as start");
$end =~ /^[+]?\d+$/ and $end > 0 or
$self->throw("Need at least a positive integer start value as end");
$end >= $start or
$self->throw("End position has to be larger or equal to start");
$end <= $self->length or
$self->throw("End position can not be larger than sequence length");
my $new = $self->SUPER::trunc($start, $end);
$start--;
map {
$new->{_meta}->{$_} = [@{$self->{_meta}->{$_}}[$start..$end]]
} keys %{$self->{_meta}};
return $new;} | General documentation
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.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
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/
| AUTHOR - Heikki Lehvaslaiho | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::PrimarySeqI methods | Top |