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Summary

Bio::LiveSeq::Translation - Translation class for LiveSeq

Package variables

Included modules

Inherit

Bio::LiveSeq::Transcript

Synopsis

  #documentation needed

Description

This stores informations about aminoacids translations of transcripts.
The implementation is that a Translation object is the translation of
a Transcript object, with different possibilities of manipulation,
different coordinate system and eventually its own ranges (protein domains).

Methods

Methods description

  Title   : aa_ranges
  Usage   : @proteinfeatures = $translation->aa_ranges()
  Function: to retrieve all the LiveSeq AARange objects attached to a
            Translation, usually created out of a SwissProt database entry
            crossreferenced from an EMBL CDS feature.
  Returns : an array
  Args    : none

  Title   : valid
  Usage   : $transcript = $obj->get_Transcript()
  Function: retrieves the reference to the object of class Transcript (if any)
            attached to a LiveSeq object
  Returns : object reference
  Args    : none

  Title   : new
  Usage   : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr);

  Function: generates a new Bio::LiveSeq::Translation
  Returns : reference to a new object of class Translation
  Errorcode -1
  Args    : reference to an object of class Transcript

Methods code

sub aa_ranges {

  my $self=shift;
  return ($self->{'aa_ranges'});

}

sub all_labels {

  my $self=shift;
  return $self->get_Transcript->all_labels;
}

# counts in triplet. Only a label matching the beginning of a triplet coding
# for an aminoacid is considered valid when setting coordinate_start
# (i.e. only in frame!)

}

sub change {

  my ($self)=@_;
  $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!");
  return (-1);

}

sub end {

  my $self=shift;
  return ($self->{'transcript'}->end);

}

sub get_Transcript {

  my $self=shift;
  return ($self->{'transcript'});
}

# These get redefined here, overriding the SeqI ones

}

sub label {

  my ($self,$position)=@_;
  my $firstlabel=$self->coordinate_start; # this is in_frame checked
  if ($position > 0) {
    $position=$position*3-2;
  } else { # if position = 0 this will be caught by Transcript, error thrown
    $position=$position*3;
  }
  return $self->get_Transcript->label($position,$firstlabel);
  # check for coord_start different
}

# returns position (aminoacids numbering) of a particular label
# used to return 0 for not in frame labels
# now returns the position anyway (after version 1.66)

}

sub labelchange {

  my ($self)=@_;
  $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!");
  return (-1);
}

# this just returns the translation of the transcript, without checking for
# stop codons

}

sub labelsubseq {

  my ($self,$start,$length,$end)=@_;
  my ($pos1,$pos2);
  my $transcript=$self->get_Transcript;
  if ($start) {
    unless ($transcript->valid($start)) {
      $self->warn("Start label not valid"); return (-1);
    }
    $pos1=$self->position($start);
  }
  if ($end) {
    if ($end == $start) {
      $length=1;
    } else {
      unless ($transcript->valid($end)) {
	$self->warn("End label not valid"); return (-1);
      }
      unless ($transcript->follows($start,$end) == 1) {
	$self->warn("End label does not follow Start label!"); return (-1);
      }
      $pos2=$self->position($end);
      $length=$pos2-$pos1+1;
    }
  }
  my $sequence=$self->seq;
  return (substr($sequence,$pos1-1,$length));
}

# return the offset in aminoacids from LiveSeq protein sequence and SwissProt
# sequence (usually as a result of an INIT_MET or a gap)

}

sub length {

  my $self=shift;
  my $seq=$self->seq;
  my $length=length($seq);
  return $length;

}

sub new {

  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my ($obj,%translation);

  my $transcript=$args{-transcript};

  $obj =\% translation;
  $obj = bless $obj, $class;

  unless ($transcript) {
    $obj->throw("$class not initialised because no -transcript given");
  }
  unless (ref($transcript) eq "Bio::LiveSeq::Transcript") {
    $obj->throw("$class not initialised because no object of class Transcript given");
  }

  #my $startbase = $transcript->start;
  #my $endbase = $transcript->end;
  my $strand = $transcript->strand;
  my $seq = $transcript->{'seq'};

  $obj->{'strand'}=$strand;
  $obj->{'seq'}=$seq;
  $obj->{'transcript'}=$transcript;
  $obj->{'alphabet'}="protein";

  $transcript->{'translation'}=$obj;# set the Translation ref into its Transcript
  return $obj;

}

sub offset {

  my $self=shift;
  return ($self->{'offset'});
}

1;

}

sub position {

  my ($self,$label)=@_;
  my $firstlabel=$self->coordinate_start; # this is in_frame checked
  my $position=$self->get_Transcript->position($label,$firstlabel);
  use integer;
  my $modulus=$position % 3;
  if ($position == 0) {
    return (0);
  } elsif ($position > 0) {
    if ($modulus != 1) {
      $self->warn("Attention! Label $label is not in frame ". 
		  "(1st position of triplet) with protein",1) if $self->verbose > 0; # ignorable
      if ($modulus == 2) {
	return ($position / 3 + 1);
      } else { # i.e. modulus == 0
	return ($position / 3);
      }
    }
    return ($position / 3 + 1);
  } else { # pos < 0
    if ($modulus != 0) {
      $self->warn("Attention! Label $label is not in frame ".
		  "(1st position of triplet) with protein",1) if $self->verbose > 0; # ignorable
      return ($position / 3 - 1); # ok for both other positions
    }
    return ($position / 3);
  }
  $self->throw( "WEIRD: execution shouldn't have reached here");
  return (0); # this should never happen, but just in case
}

# note: it inherits subseq and labelsubseq from Transcript!

}

sub positionchange {

  my ($self)=@_;
  $self->warn("Cannot change a Translation object!\nChanges have to be issued at the nucleotide level!");
  return (-1);

}

sub seq {

  my $self=shift;
  my $proteinseq;
  my $transcript=$self->get_Transcript;
  my $translation=$transcript->translate(undef, undef, undef, 
					 $self->translation_table)->seq;
  my $stop_pos=index($translation,"*");
  if ($stop_pos == -1) { # no stop present, continue downstream
    my $downstreamseq=$transcript->downstream_seq();
    #carp "the downstream is: $downstreamseq"; # debug
    my $cdnaseq=$transcript->seq();
    my $extendedseq = new Bio::PrimarySeq(-seq => "$cdnaseq$downstreamseq",
					  -alphabet => 'dna'
					  );

    $translation=$extendedseq->translate(undef, undef, undef, 
					 $self->translation_table)->seq;
    #carp "the new translation is: $translation"; # debug
    $stop_pos=index($translation,"*");
    if ($stop_pos == -1) { # still no stop present, return warning
      $self->warn("Warning: no stop codon found in the retrieved sequence downstream of Transcript ",1);
      undef $stop_pos;
      $proteinseq=$translation;
    } else {
      $proteinseq=substr($translation,0,$stop_pos+1);
      #carp "the new stopped translation is: $proteinseq, because the stop is at position $stop_pos"; # debug
    }
  } else {
    $proteinseq=substr($translation,0,$stop_pos+1);
  }
  return $proteinseq;

}

sub start {

  my $self=shift;
  return ($self->{'transcript'}->start);

}

sub transl_seq {

  my $self=shift;
  my $transcript=$self->get_Transcript;
  my $translation=$transcript->translate(undef, undef, undef, 
					 $self->translation_table)->seq;
  return $translation;
}

# version 1.74 -> now the "*" is printed

}

sub translation_table {

  my $self=shift;
  $self->get_Transcript->translation_table(@_);
}

# returns all aminoacids "affected" i.e. all aminoacids coded by any codon
# "touched" by the range selected between the labels, even if only partially.

# it's not optimized for performance but it's useful

}

sub valid {

  my ($self,$label)=@_;
  my $i;
  my @labels=$self->get_Transcript->all_labels;
  my $length=$#labels;
  while ($i <= $length) {
    if ($label == $labels[$i]) {
      return (1); # found
    }
    $i=$i+3;
  }
  return (0); # not found
}

# returns the label to the first nucleotide of the triplet coding for $position aminoacid

}

General documentation

Email: Insana@ebi.ac.uk, jinsana@gmx.net
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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