Bio::Seq Meta
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Seq::Meta - Generic superclass for sequence objects with
residue-based meta information
Package variables
No package variables defined.
Bio::LocatableSeq Bio::Seq::MetaI
  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);
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. 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.
No description
Methods description
newcode    nextTop
 Title   : new
Usage : $metaseq = Bio::Seq::Meta->new
( -meta => 'aaaaaaaabbbbbbbb',
-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);
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 force_flush.
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 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 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 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);
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 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 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 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 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   : 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 : $meta_len = $obj->named_meta_length($name);
Function: return the number of elements in the named meta set
Returns : integer
Args : -
 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.
 Title   : _do_flush
Usage :
Function: internal method to do the force that meta values are same
length as the sequence . Called from force_flush
Returns :
Args :
 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   : 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.
 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
    $GAP = '-';
    $META_GAP = ' ';
sub new {
    my ($class, @args) = @_;

    my $self = $class->SUPER::new(@args);

    my($meta, $forceflush, $nm) =

    #$self->{'_meta'} = {};
$self->{'_meta'}->{$DEFAULT_NAME} = ""; $meta && $self->meta($meta); if ($nm && ref($nm) eq 'HASH') { while (my ($name, $meta) = each %$nm) { $self->named_meta($name, $meta); } } $forceflush && $self->force_flush($forceflush); return $self;
sub meta {
   shift->named_meta($DEFAULT_NAME, shift);
sub meta_text {
sub named_meta {
   my ($self, $name, $value) = @_;

   $name ||= $DEFAULT_NAME;
   if( defined $value) {

       $self->throw("I need a scalar value, not [". ref($value). "]")
	   if ref($value);

       # test for length
my $diff = $self->length - CORE::length($value); if ($diff > 0) { $value .= (" " x $diff); } $self->{'_meta'}->{$name} = $value; #$self->_test_gap_positions($name) if $self->verbose > 0;
} return " " x $self->length if $self->force_flush && not defined $self->{'_meta'}->{$name}; $self->_do_flush if $self->force_flush; return $self->{'_meta'}->{$name};
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;
        $self->warn("Gap mismatch [$m/$s] in column [". ($i+1). "] of [$name] meta data in seq [". $self->id. "]")
            and $success = 0
                if ($s eq $META_GAP) && $s ne $m;
    return $success;
sub named_meta_text {
sub submeta {
   shift->named_submeta($DEFAULT_NAME, @_);
sub submeta_text {
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");

    if ($value) {
        $end ||= $start+length($value)-1;
        $self->warn("You are setting meta values beyond the length of the sequence\n".
                    "[$start > ". length($self->seq)."] in sequence ". $self->id)
            if $start > length $self->seq;

        # pad meta data if needed
$self->{_meta}->{$name} = () unless defined $self->{_meta}->{$name}; if (length($self->{_meta}->{$name}) < $start) { $self->{'_meta'}->{$name} .= " " x ( $start - length($self->{'_meta'}->{$name}) -1); } my $tail = ''; $tail = substr ($self->{_meta}->{$name}, $start-1+length($value)) if length($self->{_meta}->{$name}) >= $start-1+length($value); substr ($self->{_meta}->{$name}, --$start) = $value; $self->{_meta}->{$name} .= $tail; return substr ($self->{_meta}->{$name}, $start, $end - $start + 1); } else { $end or $end = length $self->seq; # pad meta data if needed
if (length($self->{_meta}->{$name}) < $end) { $self->{'_meta'}->{$name} .= " " x ( $start - length($self->{'_meta'}->{$name})); } return substr ($self->{_meta}->{$name}, $start-1, $end - $start + 1) }
sub named_submeta_text {
sub meta_names {
    my ($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 meta_length {
   my ($self) = @_;
   return $self->named_meta_length($DEFAULT_NAME);
sub named_meta_length {
   my ($self, $name) = @_;
   $name ||= $DEFAULT_NAME;
   return length ($self->{'_meta'}->{$name});
sub force_flush {
    my ($self, $value) = @_;

    if (defined $value) {
        if ($value) {
            $self->{force_flush} = 1;
        } else {
            $self->{force_flush} = 0;

    return $self->{force_flush};
sub _do_flush {
    my ($self) = @_;

    foreach my $name ( ('DEFAULT', $self->meta_names) ) {

        # elongnation
if ($self->length > $self->named_meta_length($name)) { $self->{'_meta'}->{$name} .= $META_GAP x ($self->length - $self->named_meta_length($name)) ; } # truncation
elsif ( $self->length < $self->named_meta_length($name) ) { $self->{_meta}->{$name} = substr($self->{_meta}->{$name}, 0, $self->length-1); } }
sub is_flush {
    my ($self, $name) = shift;

    return 1 if $self->force_flush;

    my $sticky = '';

    if ($name) {
        $sticky .= "$name " if $self->length != $self->named_meta_length($name);
    } else {
        foreach my $m ($self->meta_names) {
            $sticky .= "$m " if ($self->named_meta_length($m) > 0) && ($self->length != $self->named_meta_length($m));

    if ($sticky) {
        print "These meta set are not flush: $sticky\n" if $self->verbose; 
        return 0;

    return 1;
sub revcom {
    my $self = shift;

    $self->throw("Can not get a reverse complement. The object is not flush.")
        unless $self->is_flush;

    my $new = $self->SUPER::revcom;
    foreach (keys %{$self->{_meta}}) {
        $new->named_meta($_, scalar reverse $self->{_meta}->{$_} );
    return $new;
sub trunc {
    my ($self, $start, $end) = @_;

    # test arguments
$start =~ /^[+]?\d+$/ 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); $start--; foreach (keys %{$self->{_meta}}) { $new->named_meta($_, substr($self->{_meta}->{$_}, $start, $end - $start) ); }; return $new;
sub to_string {
    my ($self) = @_;
    my $out = Bio::SeqIO->new(-format=>'metafasta');
    return 1;

General documentation
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
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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.                  - General discussion - About the mailing lists
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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 BugsTop
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
AUTHOR - Heikki LehvaslaihoTop
Email heikki-at-bioperl-dot-org
Chad Matsalla,
Aaron Mackey,
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::PrimarySeqI methodsTop