Bio PrimarySeqI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
Package variables
No package variables defined.
Included modules
    # Bio::PrimarySeqI is the interface class for sequences.
# If you are a newcomer to bioperl, you might want to start with
# Bio::Seq documentation.
# Test if this is a seq object $obj->isa("Bio::PrimarySeqI") || $obj->throw("$obj does not implement the Bio::PrimarySeqI interface"); # Accessors $string = $obj->seq(); $substring = $obj->subseq(12,50); $display = $obj->display_id(); # for human display $id = $obj->primary_id(); # unique id for this object, # implementation defined $unique_key= $obj->accession_number(); # unique biological id # Object manipulation eval { $rev = $obj->revcom(); }; if( $@ ) { $obj->throw("Could not reverse complement. ". "Probably not DNA. Actual exception\n$@\n"); } $trunc = $obj->trunc(12,50); # $rev and $trunc are Bio::PrimarySeqI compliant objects
This object defines an abstract interface to basic sequence
information - for most users of the package the documentation (and
methods) in this class are not useful - this is a developers-only
class which defines what methods have to be implmented by other Perl
objects to comply to the Bio::PrimarySeqI interface. Go "perldoc
Bio::Seq" or "man Bio::Seq" for more information on the main class for
PrimarySeq is an object just for the sequence and its name(s), nothing
more. Seq is the larger object complete with features. There is a pure
perl implementation of this in Bio::PrimarySeq. If you just want to
use Bio::PrimarySeq objects, then please read that module first. This
module defines the interface, and is of more interest to people who
want to wrap their own Perl Objects/RDBs/FileSystems etc in way that
they "are" bioperl sequence objects, even though it is not using Perl
to store the sequence etc.
This interface defines what bioperl considers necessary to "be" a
sequence, without providing an implementation of this, an
implementation is provided in Bio::PrimarySeq. If you want to provide
a Bio::PrimarySeq-compliant object which in fact wraps another
object/database/out-of-perl experience, then this is the correct thing
to wrap, generally by providing a wrapper class which would inherit
from your object and this Bio::PrimarySeqI interface. The wrapper class
then would have methods lists in the "Implementation Specific
Functions" which would provide these methods for your object.
No description
No description
No description
Methods description
seqcode    nextTop
 Title   : seq
Usage : $string = $obj->seq()
Function: Returns the sequence as a string of letters. The
case of the letters is left up to the implementer.
Suggested cases are upper case for proteins and lower case for
DNA sequence (IUPAC standard), but implementations are suggested to
keep an open mind about case (some users... want mixed case!)
Returns : A scalar
Status : Virtual
 Title   : subseq
Usage : $substring = $obj->subseq(10,40);
Function: Returns the subseq from start to end, where the first base
is 1 and the number is inclusive, i.e. 1-2 are the first two
bases of the sequence.
Start cannot be larger than end but can be equal. Returns : A string Args : Status : Virtual
 Title   : display_id
Usage : $id_string = $obj->display_id();
Function: Returns the display id, also known as the common name of the Sequence
The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience reasons. Returns : A string Args : None Status : Virtual
 Title   : accession_number
Usage : $unique_biological_key = $obj->accession_number;
Function: Returns the unique biological id for a sequence, commonly
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
unique id for the implemetation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return "unknown". Returns : A string Args : None Status : Virtual
 Title   : primary_id
Usage : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
implementation. This allows implementations to manage their
own object ids in a way the implementaiton can control
clients can expect one id to map to one object.
For sequences with no accession number, this method should return a stringified memory location. Returns : A string Args : None Status : Virtual
 Title   : can_call_new
Usage : if( $obj->can_call_new ) {
$newobj = $obj->new( %param );
Function: Can_call_new returns 1 or 0 depending
on whether an implementation allows new
constructor to be called. If a new constructor
is allowed, then it should take the followed hashed
constructor list.
$myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -alphabet => 'dna', ); Returns : 1 or 0 Args :
 Title   : alphabet
Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of sequence being one of
'dna', 'rna' or 'protein'. This is case sensitive.
This is not called "type" because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : A string either 'dna','rna','protein'. NB - the object must make a call of the alphabet, if there is no alphabet specified it has to guess. Args : None Status : Virtual
 Title   : moltype
Usage : Deprecated. Use alphabet() instead.
 Title   : revcom
Usage : $rev = $seq->revcom()
Function: Produces a new Bio::PrimarySeqI implementing object which
is the reversed complement of the sequence. For protein
sequences this throws an exception of "Sequence is a
protein. Cannot revcom".
The id is the same id as the original sequence, and the accession number is also indentical. If someone wants to track that this sequence has be reversed, it needs to define its own extensionsj. To do an inplace edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::PrimarySeqI object Args : None
 Title   : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence.
Returns : A fresh Bio::PrimarySeqI implementing object.
Args : Two integers denoting first and last base of the sub-sequence.
 Title   : translate
Usage : $protein_seq_obj = $dna_seq_obj->translate
Or if you expect a complete coding sequence (CDS) translation, with initiator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); Or if you want translate() to find the first initiation codon and return the corresponding protein: $protein_seq_obj = $cds_seq_obj->translate(-orf => 1); Function: Provides the translation of the DNA sequence using full IUPAC ambiguities in DNA/RNA and amino acid codes. The complete CDS translation is identical to EMBL/TREMBL database translation. Note that the trailing terminator character is removed before returning the translated protein object. Note: if you set $dna_seq_obj->verbose(1) you will get a warning if the first codon is not a valid initiator. Returns : A Bio::PrimarySeqI implementing object Args : -terminator character for terminator, default '*' -unknown character for unknown, default 'X' -frame positive integer frame shift (in bases), default 0 -codontable_id integer codon table id, default 1 -complete boolean, if true, complete CDS is expected. default false -complete_codons boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. For instance, if the incomplete codon is 'GG', the completed codon is 'GGN', which is glycine (G). Defaults to 'false'; setting '-complete' also makes this true. -throw boolean, throw exception if ORF not complete, default false -orf if 'longest', find longest ORF. other true value, find first ORF. default 0 -codontable optional Bio::Tools::CodonTable object to use for
optional three-character string to force as initiation
codon (e.g. 'atg'). If unset, start codons are
determined by the CodonTable. Case insensitive.
optional positive integer offset for fuzzy locations.
if set, must be either 1, 2, or 3
 Title   : transcribe
Usage : $xseq = $seq->transcribe
Function: Convert base T to base U
Returns : PrimarySeqI object of alphabet 'rna' or
undef if $seq->alphabet ne 'dna'
Args :
 Title   : rev_transcribe
Usage : $rtseq = $seq->rev_transcribe
Function: Convert base U to base T
Returns : PrimarySeqI object of alphabet 'dna' or
undef if $seq->alphabet ne 'rna'
Args :
 Title   : id
Usage : $id = $seq->id()
Function: ID of the sequence. This should normally be (and actually is in
the implementation provided here) just a synonym for display_id().
Returns : A string.
Args :
 Title   : length
Usage : $len = $seq->length()
Returns : Integer representing the length of the sequence.
Args :
 Title   : desc
Usage : $seq->desc($newval);
$description = $seq->desc();
Function: Get/set description text for a seq object
Returns : Value of desc
Args : newvalue (optional)
 Title   : is_circular
Usage : if( $obj->is_circular) { /Do Something/ }
Function: Returns true if the molecule is circular
Returns : Boolean value
Args : none
 Title   : _find_orfs_nucleotide
Usage :
Function: Finds ORF starting at 1st initiation codon in nucleotide sequence.
The ORF is not required to have a termination codon.
Example :
Returns : a list of string coordinates of ORF locations (0-based half-open),
sorted descending by length (so that the longest is first)
as: [ start, end, frame, length ], [ start, end, frame, length ], ...
Args : Nucleotide sequence,
CodonTable object,
(optional) alternative initiation codon (e.g. 'ATA'),
(optional) boolean that, if true, stops after finding the
first available ORF
 Title   : _attempt_to_load_Seq
Usage :
Example :
Returns :
Args :
Methods code
sub seq {
   my ($self) = @_;
sub subseq {
   my ($self) = @_;
sub display_id {
   my ($self) = @_;
sub accession_number {
   my ($self,@args) = @_;
sub primary_id {
   my ($self,@args) = @_;
sub can_call_new {
   my ($self,@args) = @_;

   # we default to 0 here
return 0;
sub alphabet {
    my ( $self ) = @_;
sub moltype {
   my ($self,@args) = @_;

   $self->warn("moltype: pre v1.0 method. Calling alphabet() instead...");
sub revcom {
   my ($self) = @_;

   my $seqclass;
   if($self->can_call_new()) {
       $seqclass = ref($self);
   } else {
       $seqclass = 'Bio::PrimarySeq';
   my $out = $seqclass->new( '-seq' => $self->_revcom_from_string($self->seq, $self->alphabet),
			     '-is_circular'  => $self->is_circular,
			     '-display_id'  => $self->display_id,
			     '-accession_number' => $self->accession_number,
			     '-alphabet' => $self->alphabet,
			     '-desc' => $self->desc(),
                             '-verbose' => $self->verbose
   return $out;
sub _revcom_from_string {
   my ($self, $string, $alphabet) = @_;

   # Check that reverse-complementing makes sense
if( $alphabet eq 'protein' ) { $self->throw("Sequence is a protein. Cannot revcom."); } if( $alphabet ne 'dna' && $alphabet ne 'rna' ) { my $msg = "Sequence is not dna or rna, but [$alphabet]. Attempting to revcom, ". "but unsure if this is right."; if( $self->can('warn') ) { $self->warn($msg); } else { warn("[$self] $msg"); } } # If sequence is RNA, map to DNA (then map back later)
if( $alphabet eq 'rna' ) { $string =~ tr/uU/tT/; } # Reverse-complement now
$string =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; $string = CORE::reverse $string; # Map back RNA to DNA
if( $alphabet eq 'rna' ) { $string =~ tr/tT/uU/; } return $string;
sub trunc {
   my ($self,$start,$end) = @_;

   my $str;
   if( defined $start && ref($start) &&
       $start->isa('Bio::LocationI') ) {
       $str = $self->subseq($start); # start is a location actually
} elsif( !$end ) { $self->throw("trunc start,end -- there was no end for $start"); } elsif( $end < $start ) { my $msg = "start [$start] is greater than end [$end].\n ". "If you want to truncated and reverse complement,\n ". "you must call trunc followed by revcom. Sorry."; $self->throw($msg); } else { $str = $self->subseq($start,$end); } my $seqclass; if($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-seq' => $str, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, '-alphabet' => $self->alphabet, '-desc' => $self->desc(), '-verbose' => $self->verbose ); return $out;
sub translate {
	 my ($self,@args) = @_;
     my ($terminator, $unknown, $frame, $codonTableId, $complete,
     $complete_codons, $throw, $codonTable, $orf, $start_codon, $offset);

	 ## new API with named parameters, post 1.5.1
if ($args[0] && $args[0] =~ /^-[A-Z]+/i) { ($terminator, $unknown, $frame, $codonTableId, $complete, $complete_codons, $throw,$codonTable, $orf, $start_codon, $offset) = $self->_rearrange([qw(TERMINATOR UNKNOWN FRAME CODONTABLE_ID COMPLETE COMPLETE_CODONS THROW CODONTABLE ORF START OFFSET)], @args); ## old API, 1.5.1 and preceding versions
} else { ($terminator, $unknown, $frame, $codonTableId, $complete, $throw, $codonTable, $offset) = @args; } ## Initialize termination codon, unknown codon, codon table id, frame
$terminator = '*' unless (defined($terminator) and $terminator ne ''); $unknown = "X" unless (defined($unknown) and $unknown ne ''); $frame = 0 unless (defined($frame) and $frame ne ''); $codonTableId = 1 unless (defined($codonTableId) and $codonTableId ne ''); $complete_codons ||= $complete || 0; ## Get a CodonTable, error if custom CodonTable is invalid
if ($codonTable) { $self->throw("Need a Bio::Tools::CodonTable object, not ". $codonTable) unless $codonTable->isa('Bio::Tools::CodonTable'); } else { # shouldn't this be cached? Seems wasteful to have a new instance
# every time...
$codonTable = Bio::Tools::CodonTable->new( -id => $codonTableId); } ## Error if alphabet is "protein"
$self->throw("Can't translate an amino acid sequence.") if ($self->alphabet =~ /protein/i); ## Error if -start parameter isn't a valid codon
if ($start_codon) { $self->throw("Invalid start codon: $start_codon.") if ( $start_codon !~ /^[A-Z]{3}$/i ); } my $seq; if ($offset) { $self->throw("Offset must be 1, 2, or 3.") if ( $offset !~ /^[123]$/ ); my ($start, $end) = ($offset, $self->length); ($seq) = $self->subseq($start, $end); } else { ($seq) = $self->seq(); } ## ignore frame if an ORF is supposed to be found
if ( $orf ) { my ($orf_region) = $self->_find_orfs_nucleotide( $seq, $codonTable, $start_codon, $orf eq 'longest' ? 0 : 'first_only' ); $seq = $self->_orf_sequence( $seq, $orf_region ); } else { ## use frame, error if frame is not 0, 1 or 2
$self->throw("Valid values for frame are 0, 1, or 2, not $frame.") unless ($frame == 0 or $frame == 1 or $frame == 2); $seq = substr($seq,$frame); } ## Translate it
my $output = $codonTable->translate($seq, $complete_codons); # Use user-input terminator/unknown
$output =~ s/\*/$terminator/g; $output =~ s/X/$unknown/g; ## Only if we are expecting to translate a complete coding region
if ($complete) { my $id = $self->display_id; # remove the terminator character
if( substr($output,-1,1) eq $terminator ) { chop $output; } else { $throw && $self->throw("Seq [$id]: Not using a valid terminator codon!"); $self->warn("Seq [$id]: Not using a valid terminator codon!"); } # test if there are terminator characters inside the protein sequence!
if ($output =~ /\Q$terminator\E/) { $id ||= ''; $throw && $self->throw("Seq [$id]: Terminator codon inside CDS!"); $self->warn("Seq [$id]: Terminator codon inside CDS!"); } # if the initiator codon is not ATG, the amino acid needs to be changed to M
if ( substr($output,0,1) ne 'M' ) { if ($codonTable->is_start_codon(substr($seq, 0, 3)) ) { $output = 'M'. substr($output,1); } elsif ($throw) { $self->throw("Seq [$id]: Not using a valid initiator codon!"); } else { $self->warn("Seq [$id]: Not using a valid initiator codon!"); } } } my $seqclass; if ($self->can_call_new()) { $seqclass = ref($self); } else { $seqclass = 'Bio::PrimarySeq'; $self->_attempt_to_load_Seq(); } my $out = $seqclass->new( '-seq' => $output, '-display_id' => $self->display_id, '-accession_number' => $self->accession_number, # is there anything wrong with retaining the
# description?
'-desc' => $self->desc(), '-alphabet' => 'protein', '-verbose' => $self->verbose ); return $out;
sub transcribe {
    my $self = shift;
    return unless $self->alphabet eq 'dna';
    my $s = $self->seq;
    $s =~ tr/tT/uU/;
    my $class;
    if ($self->can_call_new) {
	$class = ref($self);
    } else {
	$class = 'Bio::PrimarySeq';
    my $desc = $self->desc || '';
    return $class->new(
	'-seq' => $s,
	'-alphabet' => 'rna',
	'-display_id'  => $self->display_id,
	'-accession_number' => $self->accession_number,
	'-desc' => "${desc}[TRANSCRIBED]",
	'-verbose' => $self->verbose
sub rev_transcribe {
    my $self = shift;
    return unless $self->alphabet eq 'rna';
    my $s = $self->seq;
    $s =~ tr/uU/tT/;
    my $class;
    if ($self->can_call_new) {
	$class = ref($self);
    } else {
	$class = 'Bio::PrimarySeq';
    return $class->new(
	'-seq' => $s,
	'-alphabet' => 'dna',
	'-display_id'  => $self->display_id,
	'-accession_number' => $self->accession_number,
	'-desc' => $self->desc . "[REVERSE TRANSCRIBED]",
	'-verbose' => $self->verbose
sub id {
   my ($self)= @_;

   return $self->display_id();
sub length {
   my ($self)= @_;
sub desc {
sub is_circular {
sub _find_orfs_nucleotide {
    my ( $self, $sequence, $codon_table, $start_codon, $first_only ) = @_;
    $sequence    = uc $sequence;
    $start_codon = uc $start_codon if $start_codon;

    my $is_start = $start_codon
        ? sub { shift eq $start_codon }
        : sub { $codon_table->is_start_codon( shift ) };

    # stores the begin index of the currently-running ORF in each
# reading frame
my @current_orf_start = (-1,-1,-1); #< stores coordinates of longest observed orf (so far) in each
# reading frame
my @orfs; # go through each base of the sequence, and each reading frame for each base
my $seqlen = CORE::length $sequence; for( my $j = 0; $j <= $seqlen-3; $j++ ) { my $frame = $j % 3; my $this_codon = substr( $sequence, $j, 3 ); # if in an orf and this is either a stop codon or the last in-frame codon in the string
if ( $current_orf_start[$frame] >= 0 ) { if ( $codon_table->is_ter_codon( $this_codon ) ||( my $is_last_codon_in_frame = ($j >= $seqlen-5)) ) { # record ORF start, end (half-open), length, and frame
my @this_orf = ( $current_orf_start[$frame], $j+3, undef, $frame ); my $this_orf_length = $this_orf[2] = ( $this_orf[1] - $this_orf[0] ); $self->warn( "Translating partial ORF " .$self->_truncate_seq( $self->_orf_sequence( $sequence,\@ this_orf )) .' from end of nucleotide sequence' ) if $first_only && $is_last_codon_in_frame; return\@ this_orf if $first_only; push @orfs,\@ this_orf; $current_orf_start[$frame] = -1; } } # if this is a start codon
elsif ( $is_start->($this_codon) ) { $current_orf_start[$frame] = $j; } } return sort { $b->[2] <=> $a->[2] } @orfs;
sub _truncate_seq {
    my ($self,$seq) = @_;
    return CORE::length($seq) > 200 ? substr($seq,0,50).'...'.substr($seq,-50) : $seq;
sub _orf_sequence {
    my ($self, $seq, $orf ) = @_;
    return '' unless $orf;
    return substr( $seq, $orf->[0], $orf->[2] )
sub _attempt_to_load_Seq {
   my ($self) = @_;

   if( $main::{'Bio::PrimarySeq'} ) {
       return 1;
   } else {
       eval {
	   require Bio::PrimarySeq;
       if( $@ ) {
	   my $text = "Bio::PrimarySeq could not be loaded for [$self]\n".
	       "This indicates that you are using Bio::PrimarySeqI ".
	       "without Bio::PrimarySeq loaded or without providing a ".
	       "complete implementation.\nThe most likely problem is that there ".
	       "has been a misconfiguration of the bioperl environment\n".
	       "Actual exception:\n\n";
	   return 0;
       return 1;


General documentation
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.                  - General discussion - About the mailing lists
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 - Ewan BirneyTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Implementation Specific FunctionsTop
These functions are the ones that a specific implementation must
Optional Implementation FunctionsTop
The following functions rely on the above functions. An
implementing class does not need to provide these functions, as they
will be provided by this class, but is free to override these
The revcom(), trunc(), and translate() methods create new sequence
objects. They will call new() on the class of the sequence object
instance passed as argument, unless can_call_new() returns FALSE. In
the latter case a Bio::PrimarySeq object will be created. Implementors
which really want to control how objects are created (eg, for object
persistence over a database, or objects in a CORBA framework), they
are encouraged to override these methods
The -start argument only applies when -orf is set to 1. By default all
initiation codons found in the given codon table are used but when
"start" is set to some codon this codon will be used exclusively as
the initiation codon. Note that the default codon table (NCBI
"Standard") has 3 initiation codons!
By default translate() translates termination codons to the some
character (default is *), both internal and trailing codons. Setting
"-complete" to 1 tells translate() to remove the trailing character.
-offset is used for seqfeatures which contain the the \codon_start tag
and can be set to 1, 2, or 3. This is the offset by which the
sequence translation starts relative to the first base of the feature
For details on codon tables used by translate() see Bio::Tools::CodonTable.
Deprecated argument set (v. 1.5.1 and prior versions) where each argument is an
element in an array:
  1: character for terminator (optional), defaults to '*'.
2: character for unknown amino acid (optional), defaults to 'X'.
3: frame (optional), valid values are 0, 1, 2, defaults to 0.
4: codon table id (optional), defaults to 1.
5: complete coding sequence expected, defaults to 0 (false).
6: boolean, throw exception if not complete coding sequence
(true), defaults to warning (false)
7: codontable, a custom Bio::Tools::CodonTable object (optional).
Private functionsTop
These are some private functions for the PrimarySeqI interface. You do not
need to implement these functions