Bio::Seq EncodedSeq
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Summary
Bio::Seq::EncodedSeq - subtype of Bio::LocatableSeq to store DNA that encodes a protein
Package variables
No package variables defined.
Inherit
Bio::LocatableSeq
Synopsis
  $obj = Bio::Seq::EncodedSeq->new(-seq => $dna,
-encoding => "CCCCCCCIIIIICCCCC",
-start => 1,
-strand => 1,
-length => 17);
# splice out (and possibly revcomp) the coding sequence $cds = obj->cds; # obtain the protein translation of the sequence $prot = $obj->translate; # other access/inspection routines as with Bio::LocatableSeq and # Bio::SeqI; note that coordinates are relative only to the DNA # sequence, not it's implicit encoded protein sequence.
Description
Bio::Seq::EncodedSeq is a Bio::LocatableSeq
object that holds a DNA sequence as well as information about the
coding potential of that DNA sequence. It is meant to be useful in an
alignment context, where the DNA may contain frameshifts, gaps and/or
introns, or in describing the transcript of a gene. An EncodedSeq
provides the ability to access the "spliced" coding sequence, meaning
that all introns and gaps are removed, and any frameshifts are
adjusted to provide a "clean" CDS.
In order to make simultaneous use of either the DNA or the implicit
encoded protein sequence coordinates, please see
Bio::Coordinate::EncodingPair.
Methods
newDescriptionCode
encodingDescriptionCode
_convert2implicit
No description
Code
_recheck_encoding
No description
Code
cdsDescriptionCode
translateDescriptionCode
protseqDescriptionCode
dnaseqDescriptionCode
trunc
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : $obj = Bio::Seq::EncodedSeq->new(-seq => "AGTACGTGTCATG",
-encoding => "CCCCCCFCCCCCC",
-id => "myseq",
-start => 1,
-end => 13,
-strand => 1
);
Function: creates a new Bio::Seq::EncodedSeq object from a supplied DNA
sequence
Returns : a new Bio::Seq::EncodedSeq object
Args : seq - primary nucleotide sequence used to encode the protein; note that any positions involved in a gap ('G') or backward frameshift ('B') should have one or more gap characters; if the encoding specifies G or B, but no (or not enough) gap characters exist, *they'll be added*; similary, if there are gap characters without a corresponding G or B encoding, G's will be inserted into the encoding. This allows some flexibility in specifying your sequence and coding without having to calculate a lot of the encoding for yourself. encoding - a string of characters (see Encoding Table) describing backwards frameshifts implied by the encoding but not present in the sequence will be added (as '-'s) to the sequence. If not supplied, it will be assumed that all positions are coding (C). Encoding may include either implicit phase encoding characters (i.e. "CCC") and/or explicit encoding characters (i.e. "CDE"). Additionally, prefixed numbers may be used to denote repetition (i.e. "27C3I28C"). Alternatively, encoding may be a hashref datastructure, with encoding characters as keys and Bio::LocationI objects (or arrayrefs of Bio::LocationI objects) as values, e.g.: { C => [ Bio::Location::Simple->new(1,9), Bio::Location::Simple->new(11,13) ], F => Bio::Location::Simple->new(10,10), } # same as "CCCCCCCCCFCCC" Note that if the location ranges overlap, the behavior of the encoding will be undefined (well, it will be defined, but only according to the order in which the hash keys are read, which is basically undefined ... just don't do that). id, start, end, strand - as with Bio::LocatableSeq; note that the coordinates are relative to the encoding DNA sequence, not the implicit protein sequence. If strand is reversed, then the encoding is assumed to be relative to the reverse strand as well.
encodingcodeprevnextTop
 Title   : encoding
Usage : $obj->encoding("CCCCCC");
$obj->encoding( -encoding => { I => $location } );
$enc = $obj->encoding(-explicit => 1);
$enc = $obj->encoding("CCCCCC", -explicit => 1);
$enc = $obj->encoding(-location => $location,
-explicit => 1,
-absolute => 1 );
Function: get/set the objects encoding, either globally or by location(s).
Returns : the (possibly new) encoding string.
Args : encoding - see the encoding argument to the new() function.
explicit - whether or not to return explicit phase information in the coding (i.e. "CCC" becomes "CDE", "III" becomes "IJK", etc); defaults to 0. location - optional; location to get/set the encoding. Defaults to the entire sequence. absolute - whether or not the locational elements (either in the encoding hashref or the location argument) are relative to the absolute start/end of the Bio::LocatableSeq, or to the internal, relative coordinate system (beginning at 1); defaults to 0 (i.e. relative)
cdscodeprevnextTop
 Title   : cds
Usage : $cds = $obj->cds(-nogaps => 1);
Function: obtain the "spliced" DNA sequence, by removing any
nucleotides that participate in an UTR, forward frameshift
or intron, and replacing any unknown nucleotide implied by
a backward frameshift or gap with N's.
Returns : a Bio::Seq::EncodedSeq object, with an encoding consisting only
of "CCCC..".
Args : nogaps - strip any gap characters (resulting from 'G' or 'B'
encodings), rather than replacing them with N's.
translatecodeprevnextTop
 Title   : translate
Usage : $prot = $obj->translate(@args);
Function: obtain the protein sequence encoded by the underlying DNA
sequence; same as $obj->cds()->translate(@args).
Returns : a Bio::PrimarySeq object.
Args : same as the translate() function of Bio::PrimarySeqI
protseqcodeprevnextTop
 Title   : seq
Usage : $protseq = $obj->protseq();
Function: obtain the raw protein sequence encoded by the underlying
DNA sequence; This is the same as calling
$obj->translate()->seq();
Returns : a string of single-letter amino acid codes
Args : same as the seq() function of Bio::PrimarySeq; note that this
function may not be used to set the protein sequence; see
the dnaseq() function for that.
dnaseqcodeprevnextTop
 Title   : dnaseq
Usage : $dnaseq = $obj->dnaseq();
$obj->dnaseq("ACGTGTCGT", "CCCCCCCCC");
$obj->dnaseq(-seq => "ATG",
-encoding => "CCC",
-location => $loc );
@introns = $obj->$dnaseq(-encoding => 'I')
Function: get/set the underlying DNA sequence; will overwrite any
current DNA and/or encoding information present.
Returns : a string of single-letter nucleotide codes, including any
gaps implied by the encoding.
Args : seq - the DNA sequence to be used as a replacement
encoding - the encoding of the DNA sequence (see the new()
constructor); defaults to all 'C' if setting a
new DNA sequence. If no new DNA sequence is
being provided, then the encoding is used as a
"filter" for which to return fragments of
non-overlapping DNA that match the encoding.
location - optional, the location of the DNA sequence to
get/set; defaults to the entire sequence.
Methods code
newdescriptionprevnextTop
sub new {
    my ($self, @args) = @_;
    $self = $self->SUPER::new(@args, -alphabet => 'dna');
    my ($enc) = $self->_rearrange([qw(ENCODING)], @args);
    # set the real encoding:
if ($enc) { $self->encoding($enc); } else { $self->_recheck_encoding; } return $self;
}
encodingdescriptionprevnextTop
sub encoding {
    my ($self, @args) = @_;
    my ($enc, $loc, $exp, $abs) = $self->_rearrange([qw(ENCODING LOCATION EXPLICIT ABSOLUTE)], @args);

    if (!$enc) {
	# do nothing; _recheck_encoding will fix for us, if necessary
} elsif (ref $enc eq 'HASH') { $self->throw( -class => 'Bio::Root::NotImplemented', -text => "Hashref functionality not yet implemented;\nplease email me if you really need this."); #TODO: finish all this
while (my ($char, $locs) = each %$enc) { if (ref $locs eq 'ARRAY') { } elsif (UNIVERSAL::isa($locs, "Bio::LocationI")) { } else { $self->throw("Only a scalar or a ref to a hash; not a ref to a @{{lc ref $enc}}"); } } } elsif (! ref $enc) { $enc = uc $enc; $exp = 1 if (!defined $exp && $enc =~ m/[DEJKV]/o);
if ($enc =~ m/\d/o) { # numerically "enhanced" encoding
my
$numenc = $enc;
$enc = ''; while ($numenc =~ m/\G(\d*)([CDEIJKUVGFB])/g) {
my (
$num, $char) = ($1, $2);
$num = 1 unless $num; $enc .= $char x $num; } } if (defined $exp && $exp == 0 && $enc =~ m/([^CIUGFB])/) {
$self->throw("Unrecognized character '$1' in implicit encoding");
} elsif ($enc =~ m/[^CDEIJKUVGFB]/) {
$self->throw("Unrecognized character '$1' in explicit encoding");
} if ($loc) { # a global location, over which to apply the specified encoding.
# balk if too many non-gap characters present in encoding:
my ($ct) = $enc =~ tr/GB/GB/; $ct = length($enc) - $ct; $self->throw("Location length doesn't match number of coding chars in encoding!") if ($loc->location_type eq 'EXACT' && $loc->length != $ct); my $start = $loc->start; my $end = $loc->end; # strip any encoding that hangs off the ends of the sequence:
if ($start < $self->start) { my $diff = $self->start - $start; $start = $self->start; $enc = substr($enc, $diff); } if ($end > $self->end) { my $diff = $end - $self->end; $end = $self->end; $enc = substr($enc, -$diff); } my $currenc = $self->{_encoding}; my $currseq = $self->seq; my ($spanstart, $spanend) = ($self->column_from_residue_number($start), $self->column_from_residue_number($end) ); if ($currseq) { # strip any gaps in sequence spanned by this location:
($spanstart, $spanend) = ($spanend, $spanstart) if $self->strand < 0; my ($before, $in, $after) = $currseq =~ m/(.{@{[ $spanstart - ($loc->location_type eq 'IN-BETWEEN' ? 0 : 1) ]}})
(.{@{[ $spanend - $spanstart + ($loc->location_type eq 'IN-BETWEEN' ? -1 : 1) ]}})
(.*)
/x;
$in ||= ''; $in =~ s/[\.\-]+//g; $currseq = ($before||'') . $in. ($after||''); # change seq without changing the alphabet
$self->seq($currseq,$self->alphabet()); } $currenc = reverse $currenc if $self->strand < 0; substr($currenc, $spanstart, $spanend - $spanstart + ($loc->location_type eq 'IN-BETWEEN' ? -1 : 1), $self->strand >= 0 ? $enc : reverse $enc); $currenc = reverse $currenc if $self->strand < 0; $self->{_encoding} = $currenc; $self->_recheck_encoding; $currenc = $self->{_encoding}; $currenc = reverse $currenc if $self->strand < 0; $enc = substr($currenc, $spanstart, length $enc); $enc = reverse $enc if $self->strand < 0; return $exp ? $enc: $self->_convert2implicit($enc); } else { # presume a global redefinition; strip any current gap
# characters in the sequence so they don't corrupt the
# encoding
my $dna = $self->seq; $dna =~ s/[\.\-]//g; $self->seq($dna, 'dna'); $self->{_encoding} = $enc; } } else { $self->throw("Only a scalar or a ref to a hash; not a ref to a @{{lc ref $enc}}"); } $self->_recheck_encoding(); return $exp ? $self->{_encoding} : $self->_convert2implicit($self->{_encoding});
}
_convert2implicitdescriptionprevnextTop
sub _convert2implicit {
    my ($self, $enc) = @_;

    $enc =~ s/[DE]/C/g;
    $enc =~ s/[JK]/I/g;
    $enc =~ s/V/U/g;

    return $enc;
}
_recheck_encodingdescriptionprevnextTop
sub _recheck_encoding {
    my $self = shift;

    my @enc = split //, ($self->{_encoding} || '');

    my @nt = split(//, $self->SUPER::seq);
    @nt = reverse @nt if $self->strand && $self->strand < 0;

    # make sure an encoding exists!
@enc = ('C') x scalar grep { !/[\.\-]/o } @nt unless @enc; # check for gaps to be truly present in the sequence
# and vice versa
my $i; for ($i = 0 ; $i < @nt && $i < @enc ; $i++) { if ($nt[$i] =~ /[\.\-]/o && $enc[$i] !~ m/[GB]/o) {
splice(
@enc, $i, 0, 'G');
} elsif ($nt[$i] !~ /[\.\-]/o && $enc[$i] =~ m/[GB]/o) {
splice(
@nt, $i, 0, '-');
} } if ($i < @enc) { # extra encoding; presumably all gaps?
for ( ; $i < @enc ; $i++) { if ($enc[$i] =~ m/[GB]/o) {
push
@nt, '-';
} else { $self->throw("Extraneous encoding info: " . join('', @enc[$i..$#enc])); } } } elsif ($i < @nt) { for ( ; $i < @nt ; $i++) { if ($nt[$i] =~ m/[\.\-]/o) {
push
@enc, 'G';
} else { push @enc, 'C'; } } } my @cde_array = qw(C D E); my @ijk_array = qw(I J K); # convert any leftover implicit coding into explicit coding
my ($Cct, $Ict, $Uct, $Vct, $Vwarned) = (0, 0, 0, 0); for ($i = 0 ; $i < @enc ; $i++) { if ($enc[$i] =~ m/[CDE]/o) {
my
$temp_index = $Cct %3;
$enc[$i] = $cde_array[$temp_index]; $Cct++; $Ict = 0; $Uct = 1; $self->warn("3' untranslated encoding (V) seen prior to other coding symbols") if ($Vct && !$Vwarned++); } elsif ($enc[$i] =~ m/[IJK]/o) {
$enc[$i] = $ijk_array[$Ict % 3];
$Ict++; $Uct = 1; $self->warn("3' untranslated encoding (V) seen before other coding symbols") if ($Vct && !$Vwarned++); } elsif ($enc[$i] =~ m/[UV]/o) {
if (
$Uct == 1) {
$enc[$i] = 'V';
$Vct = 1; } } elsif ($enc[$i] eq 'B') { $Cct++; $Ict++ } elsif ($enc[$i] eq 'G') { # gap; leave alone
} } @nt = reverse @nt if $self->strand && $self->strand < 0; $self->{'seq'} = join('', @nt); # $self->seq(join('', @nt), 'dna');
$self->{_encoding} = join '', @enc;
}
cdsdescriptionprevnextTop
sub cds {
    my ($self, @args) = @_;

    my ($nogaps, $loc) = $self->_rearrange([qw(NOGAPS LOCATION)], @args);
    $nogaps = 0 unless defined $nogaps;

    my @nt = split //, $self->strand < 0 ? $self->revcom->seq : $self->seq;
    my @enc = split //, $self->_convert2implicit($self->{_encoding});

    my ($start, $end) = (0, scalar @nt);

    if ($loc) {
	$start = $loc->start;
	$start++ if $loc->location_type eq 'IN-BETWEEN';
	$start = $self->column_from_residue_number($start);
	$start--;

	$end = $loc->end;
	$end = $self->column_from_residue_number($end);

	($start, $end) = ($end, $start) if $self->strand < 0;
	$start--;
    }

    for (my $i = $start ; $i < $end ; $i++) {
	if ($enc[$i] eq 'I' || $enc[$i] eq 'U' || $enc[$i] eq 'F') {
	    # remove introns, untranslated and forward frameshift nucleotides
$nt[$i] = undef; } elsif ($enc[$i] eq 'G' || $enc[$i] eq 'B') { # replace gaps and backward frameshifts with N's, unless asked not to.
$nt[$i] = $nogaps ? undef : 'N'; } } return ($self->can_call_new ? ref($self) : __PACKAGE__)->new (-seq => join('', grep { defined } @nt[$start..--$end]), -start => $self->start, -end => $self->end, -strand => 1, -alphabet => 'dna');
}
translatedescriptionprevnextTop
sub translate {
 shift->cds(-nogaps => 1, @_)->SUPER::translate(@_) };
}
protseqdescriptionprevnextTop
sub protseq {
 shift->cds(-nogaps => 1, @_)->SUPER::translate(@_)->seq };
}
dnaseqdescriptionprevnextTop
sub dnaseq {
    my ($self, @args) = @_;
    my ($seq, $enc, $loc) = $self->_rearrange([qw(DNASEQ ENCODING LOCATION)], @args);

    $self

}

# need to overload this so that we truncate both the seq and the encoding!
}
truncdescriptionprevnextTop
sub trunc {
    my ($self, $start, $end) = @_;
    my $new = $self->SUPER::trunc($start, $end);
    $start--;
    my $enc = $self->{_encoding};
    $enc = reverse $enc if $self->strand < 0;
    $enc = substr($enc, $start, $end - $start);
    $enc = reverse $enc if $self->strand < 0;
    $new->encoding($enc);
    return $new;
}

1;
}
General documentation
ENCODINGTop
We use the term "encoding" here to refer to the series of symbols that
we use to identify which residues of a DNA sequence are protein-coding
(i.e. part of a codon), intronic, part of a 5' or 3', frameshift
"mutations", etc. From this information, a Bio::Seq::EncodedSeq is
able to "figure out" its translational CDS. There are two sets of
coding characters, one termed "implicit" and one termed "explicit".
The "implicit" encoding is a bit simpler than the "explicit" encoding:
'C' is used for any nucleotide that's part of a codon, 'U' for any
UTR, etc. The full list is shown below:
 Code  Meaning
---- -------
C coding
I intronic
U untranslated
G gapped (for use in alignments)
F a "forward", +1 frameshift
B a "backward", -1 frameshift
The "explicit" encoding is just an expansion of the "implicit"
encoding, to denote phase:
 Code  Meaning
---- -------
C coding, 1st codon position
D coding, 2nd codon position
E coding, 3rd codon position
I intronic, phase 0 (relative to intron begin) J intronic, phase 1 K intronic, phase 2 U untranslated 3'UTR V untranslated 5'UTR G gapped (for use in alignments) F a "forward", +1 frameshift B a "backward", -1 frameshift
Note that the explicit coding is meant to provide easy access to
position/phase specific nucleotides:
  $obj = Bio::Seq::EncodedSeq->new(-seq => "ACAATCAGACTACG...",
-encoding => "CCCCCCIII..."
);
# fetch arrays of nucleotides at each codon position: my @pos1 = $obj->dnaseq(encoding => 'C', explicit => 1); my @pos2 = $obj->dnaseq(encoding => 'D'); my @pos3 = $obj->dnaseq(encoding => 'E'); # fetch arrays of "3-1" codon dinucleotides, useful for genomic # signature analyses without compounding influences of codon bias: my @pairs = $obj->dnaseq(encoding => 'EC');
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 - Aaron MackeyTop
Email amackey@virginia.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _