Summary

Bio::Seq::MetaI - Generic superclass for sequence objects with
residue-based meta information

Package variables

Included modules

Inherit

Bio::LocatableSeq Bio::Seq::MetaI

Synopsis

  use Bio::LocatableSeq;
  use Bio::Seq::Meta;
  use Bio::Tools::OddCodes;
  use Bio::SeqIO;

  my $seq = Bio::LocatableSeq->new(-id=>'test',
                                   -seq=>'ACTGCTAGCT',
                                   -start=>2434,
                                   -start=>2443,
                                   -strand=>1,
                                   -verbose=>1, # to see warnings
                                  );

  bless $seq, Bio::Seq::Meta;
  # 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');

  # 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).
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
meta information 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. 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.

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 : 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);
 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

 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 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 = ' ';

}

sub new {

    my ($class, @args) = @_;

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

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

    #$self->{'_meta'} = {};
    $self->{'_meta'}->{$DEFAULT_NAME} = undef;

    $meta && $self->meta($meta);

    return $self;

}

sub meta {

   shift->named_meta($DEFAULT_NAME, shift);

}

sub meta_text {

    shift->meta(shift);

}

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 $self->verbose > 0;
   }
   return substr($self->{'_meta'}->{$name}, 0, $self->length)
       if defined $self->{'_meta'}->{$name} and
           CORE::length($self->{'_meta'}->{$name}) > $self->length;
   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;
        $self->warn("Gap mismatch [$m/$s] in column [". ($i+1). "] of [$name] meta data in seq [". $self->id. "]")
            and $success = 0
                #if ($s eq $GAP || $m eq $GAP) && $s ne $m;
                if ($s eq $META_GAP) && $s ne $m;
    }
    return $success;

}

sub named_meta_text {

    shift->named_meta(@_);

}

sub submeta {

   shift->named_submeta($DEFAULT_NAME, @_);

}

sub submeta_text {

    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");

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

        # pad meta data if needed
        if (length($self->{_meta}->{$name}) < $start) {
            $self->{'_meta'}->{$name} .=  " " x ( $start - length($self->{'_meta'}->{$name}));
        }

        my $tail = substr ($self->{_meta}->{$name}, $start-1+length($value));

        substr ($self->{_meta}->{$name}, --$start) = $value;
        $self->{_meta}->{$name} .= $tail;

        return $value;

    } else {

        $end or $end = length $self->seq;
        $end = length $self->seq if $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 {

    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 = $self->SUPER::revcom;
    foreach (keys %{$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');
    $out->write_seq($self);
    return 1;
#    undef;

}

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
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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/

Email heikki@ebi.ac.uk

Chad Matsalla, bioinformatics@dieselwurks.com
Aaron Mackey, amackey@virginia.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _