Bio::Seq Meta
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Summary
Bio::Seq::Meta - Generic superclass for sequence objects with
residue-based meta information
Package variables
No package variables defined.
Inherit
Bio::LocatableSeq Bio::Seq::MetaI
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. 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.
Methods
BEGIN Code
newDescriptionCode
metaDescriptionCode
meta_textDescriptionCode
named_metaDescriptionCode
_test_gap_positionsDescriptionCode
named_meta_textDescriptionCode
submetaDescriptionCode
submeta_textDescriptionCode
named_submetaDescriptionCode
named_submeta_textDescriptionCode
meta_namesDescriptionCode
meta_lengthDescriptionCode
named_meta_lengthDescriptionCode
force_flushDescriptionCode
_do_flushDescriptionCode
is_flushDescriptionCode
revcomDescriptionCode
truncDescriptionCode
to_string
No description
Code
Methods description
newcode    nextTop
 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
metacodeprevnextTop
 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 force_flush.
Returns : meta data in a string Args : new value, string, optional
meta_textcodeprevnextTop
 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
named_metacodeprevnextTop
 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
_test_gap_positionscodeprevnextTop
 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_textcodeprevnextTop
 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
submetacodeprevnextTop
 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 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_textcodeprevnextTop
 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
named_submetacodeprevnextTop
 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
named_submeta_textcodeprevnextTop
 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
meta_namescodeprevnextTop
 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_lengthcodeprevnextTop
 Title   : meta_length()
Usage : $meeta_len = $obj->meta_length();
Function: return the number of elements in the meta set
Returns : integer
Args : -
named_meta_lengthcodeprevnextTop
 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_flushcodeprevnextTop
 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_flushcodeprevnextTop
 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 :
is_flushcodeprevnextTop
 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
revcomcodeprevnextTop
 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.
trunccodeprevnextTop
 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
BEGINTop
BEGIN {
    $DEFAULT_NAME = 'DEFAULT';
    $GAP = '-';
    $META_GAP = ' ';
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;

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

    my($meta, $forceflush, $nm) =
        $self->_rearrange([qw(META
                              FORCE_FLUSH
                              NAMED_META)],
                          @args);

    #$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 $self;
}
metadescriptionprevnextTop
sub meta {
   shift->named_meta($DEFAULT_NAME, shift);
}
meta_textdescriptionprevnextTop
sub meta_text {
    shift->meta(shift);
}
named_metadescriptionprevnextTop
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};
}
_test_gap_positionsdescriptionprevnextTop
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 $success;
}
named_meta_textdescriptionprevnextTop
sub named_meta_text {
    shift->named_meta(@_);
}
submetadescriptionprevnextTop
sub submeta {
   shift->named_submeta($DEFAULT_NAME, @_);
}
submeta_textdescriptionprevnextTop
sub submeta_text {
    shift->submeta(@_);
}
named_submetadescriptionprevnextTop
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 - $start + 1) }
}
named_submeta_textdescriptionprevnextTop
sub named_submeta_text {
    shift->named_submeta(@_);
}
meta_namesdescriptionprevnextTop
sub meta_names {
    my ($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;
}
meta_lengthdescriptionprevnextTop
sub meta_length {
   my ($self) = @_;
   return $self->named_meta_length($DEFAULT_NAME);
}
named_meta_lengthdescriptionprevnextTop
sub named_meta_length {
   my ($self, $name) = @_;
   $name ||= $DEFAULT_NAME;
   return length ($self->{'_meta'}->{$name});
}
force_flushdescriptionprevnextTop
sub force_flush {
    my ($self, $value) = @_;

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

    return $self->{force_flush};
}
_do_flushdescriptionprevnextTop
sub _do_flush {
    my ($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, $self->length-1); } }
}
is_flushdescriptionprevnextTop
sub is_flush {
    my ($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;
}
revcomdescriptionprevnextTop
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 $new;
}
truncdescriptionprevnextTop
sub trunc {
    my ($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 $new;
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self) = @_;
    my $out = Bio::SeqIO->new(-format=>'metafasta');
    $out->write_seq($self);
    return 1;
}

1;
}
General documentation
NOTETop
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.
SEE ALSOTop
Bio::LocatableSeq,
Bio::Seq::MetaI,
Bio::Seq::Meta::Array
FEEDBACKTop
Mailing ListsTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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.
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
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Chad Matsalla, bioinformatics@dieselwurks.com
Aaron Mackey, amackey@virginia.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::PrimarySeqI methodsTop