Bio::LiveSeq AARange
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Summary
Bio::LiveSeq::AARange - AARange abstract class for LiveSeq
Package variables
No package variables defined.
Inherit
Bio::LiveSeq::SeqI
Synopsis
  #documentation needed
Description
This is used as possible parent for aminoacid range object classes.
Or it can be used straight away to define aminoacid ranges. The idea
is that the ranges defined are attached to a Translation object and
they refer to its coordinate-system when they are first created (via
the new() method). When they are created they are anyway linked to
the underlying DNA LiveSeq by way of the LiveSeq labels. This allows
to preserve the ranges even if the numbering changes in the
Translation due to deletions or insertions.
The protein sequence associated with the AARange can be accessed via
the usual seq() or subseq() methods.
The start and end of the AARange in protein coordinate system can be
fetched with aa_start() and aa_end() methods. Note: the behaviour of
these methods would be influenced by the coordinate_start set in the
corresponding Translation object. This can be desirable but can also
lead to confusion if the coordinate_start had been changed and the
original position of the AARange was to be retrieved.
start() and end() methods of the AARange will point to the labels
identifying the first nucleotide of the first and last triplet coding
for the start and end of the AminoAcidRange.
The underlying nucleotide sequence of the AARange can be retrieved
with the labelsubseq() method. This would retrieve the whole DNA
sequence, including possible introns. This is called "DNA_sequence".
To fetch the nucleotide sequence of the Transcript, without introns,
the labelsubseq() of the attached Transcript (the Transcript the
Translation comes from) has to be accessed. This is called
"cDNA_sequence".
Here are the operations to retrieve these latter two kinds of
sequences:
   $startlabel=$AARange->start;
$endtripletlabel=$AARange->end;
$endlabel=$AARange->{'seq'}->label(3,$endtripletlabel,$AARange->strand);
$dnaseq=$AARange->labelsubseq($startlabel,undef,$endlabel)); $cdnaseq=$AARange->get_Transcript->labelsubseq($startlabel,undef,$endlabel);
To simplify, these operations have been included in two additional
methods: dna_seq() and cdna_seq().
These would return the whole sequence, as in the examples above. But
the above general scheme can be used by specifying different labels,
to retrieve hypothetical subsequences of interest.
Methods
newDescriptionCode
coordinate_start
No description
Code
all_labels
No description
Code
valid
No description
Code
get_TranscriptDescriptionCode
get_TranslationDescriptionCode
change
No description
Code
positionchange
No description
Code
labelchange
No description
Code
subseq
No description
Code
seq
No description
Code
length
No description
Code
label
No description
Code
position
No description
Code
aa_startDescriptionCode
aa_endDescriptionCode
dna_seqDescriptionCode
cdna_seqDescriptionCode
gene
No description
Code
Methods description
newcode    nextTop
  Title   : new
Usage : $aarange = Bio::LiveSeq::AARange->new(-translation => $obj_ref,
-start => $beginaa,
-end => $endaa,
-name => "ABCD",
-description => "DCBA",
-translength => $length);
Function: generates a new AminoAcidRange LiveSeq object Returns : reference to a new object of class AARange Errorcode -1 Args : two positions in AminoAcid coordinate numbering an object reference specifying to which translation the aminoacid ranges refer to a name and a description (optional) an optional "translength" argument: this can be given when a lot of AARanges are to be created at the same time for the same Translation object, calculating it with $translation->length This would increase the speed, avoiding the new() function to calculate everytime the same length again and again for every obj.
get_TranscriptcodeprevnextTop
  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
get_TranslationcodeprevnextTop
  Title   : valid
Usage : $translation = $obj->get_Translation()
Function: retrieves the reference to the object of class Translation (if any)
attached to a LiveSeq object
Returns : object reference
Args : none
aa_startcodeprevnextTop
  Title   : aa_start
Usage : $end = $aarange->aa_start()
Returns : integer (position, according to Translation coordinate system) of
the start of an AminoAcidRange object
Args : none
aa_endcodeprevnextTop
  Title   : aa_end
Usage : $end = $aarange->aa_end()
Returns : integer (position, according to Translation coordinate system) of
the end of an AminoAcidRange object
Args : none
dna_seqcodeprevnextTop
  Title   : dna_seq
Usage : $end = $aarange->dna_seq()
Returns : the sequence at DNA level of the entire AminoAcidRange
this would include introns (if present)
Args : none
cdna_seqcodeprevnextTop
  Title   : cdna_seq
Usage : $end = $aarange->cdna_seq()
Returns : the sequence at cDNA level of the entire AminoAcidRange
i.e. this is the part of the Transcript that codes for the
AminoAcidRange. It would be composed just of exonic DNA.
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my ($obj,%range);

  $obj =\% range;
  $obj = bless $obj, $class;
  my $self=$obj;

  my ($translation,$start,$end,$name,$description,$translength)=($args{-translation},$args{-start},$args{-end},$args{-name},$args{-description},$args{-translength});

  unless (($translation)&&(ref($translation) eq "Bio::LiveSeq::Translation")) {
    $self->warn("No -translation or wrong type given");
    return (-1);
  }
  unless ($translength) { # if it's not given, fetch it
$translength=$translation->length; } my $seq=$translation->{'seq'}; if (($start < 1)&&($start > $translength)) { $self->warn("$class not initialised because start aminoacid position not valid"); return (-1); } if (($end < 1)&&($end > $translength)) { $self->warn("$class not initialised because end aminoacid position not valid"); return (-1); } if ($start > $end) { $self->warn("$class not initialised because start position > end position!"); return (-1); } my ($starttripletlabel,$endtripletlabel); if ($start == $end) { # trick to increase speed
$starttripletlabel=$endtripletlabel=$translation->label($start); } else { ($starttripletlabel,$endtripletlabel)=($translation->label($start),$translation->label($end)); } unless (($starttripletlabel > 0)&&($endtripletlabel > 0)) { $self->warn("$class not initialised because of problems in retrieving start or end label!"); return (-1); } # unsure if needed:
#my $endlabel=$seq->label(3,$endtripletlabel); # to get the real end
#unless ($endlabel > 0) {
#carp "$class not initialised because of problems retrieving the last nucleotide of the triplet coding for the end aminoacid";
#return (-1);
#}
$self->{'seq'}=$seq; $self->{'start'}=$starttripletlabel; $self->{'end'}=$endtripletlabel; $self->{'strand'}=$translation->strand; $self->{'translation'}=$translation; $self->{'name'}=$name; $self->{'description'}=$description; $self->{'alphabet'}="protein"; return $obj;
}
coordinate_startdescriptionprevnextTop
sub coordinate_start {
  my $self=shift;
  $self->warn("Cannot perform this operation in an AminoAcidRange object!");
  return (-1);
}
all_labelsdescriptionprevnextTop
sub all_labels {
  my $self=shift;
  $self->warn("Cannot perform this operation in an AminoAcidRange object!");
  return (-1);
}
validdescriptionprevnextTop
sub valid {
  my $self=shift;
  $self->warn("Cannot perform this operation in an AminoAcidRange object!");
  return (-1);
}
get_TranscriptdescriptionprevnextTop
sub get_Transcript {
  my $self=shift;
  return ($self->get_Translation->get_Transcript);
}
get_TranslationdescriptionprevnextTop
sub get_Translation {
  my $self=shift;
  return ($self->{'translation'});
}
changedescriptionprevnextTop
sub change {
  my $self=shift;
  $self->warn("Cannot change an AminoAcidRange object!");
  return (-1);
}
positionchangedescriptionprevnextTop
sub positionchange {
  my $self=shift;
  $self->warn("Cannot change an AminoAcidRange object!");
  return (-1);
}
labelchangedescriptionprevnextTop
sub labelchange {
  my $self=shift;
  $self->warn("Cannot change an AminoAcidRange object!");
  return (-1);
}
subseqdescriptionprevnextTop
sub subseq {
  my ($self,$pos1,$pos2,$length) = @_;
  if (defined ($length)) {
    if ($length < 1) {
      $self->warn("No sense asking for a subseq of length < 1");
      return (-1);
    }
  }
  unless (defined ($pos1)) {
    $pos1=1;
  } elsif ($pos1 < 1) { # if position out of boundaries
$self->warn("Starting position for AARange cannot be < 1!"); return (-1); if ((defined ($pos2))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } } my $seq=$self->seq; my $objlength=length($seq); unless (defined ($length)) { $length=$objlength-$pos1+1; } if (defined ($pos2)) { if ($pos2 > $objlength) { # if position out of boundaries
$self->warn("Ending position for AARange cannot be > length of AARange!"); return (-1); } $length=$pos2-$pos1+1; if ((defined ($pos1))&&($pos1>$pos2)) { $self->warn("1st position($pos1) cannot be > 2nd position($pos2)!"); return (-1); } } my $str=substr($seq,$pos1-1,$length); if (length($str) < $length) { $self->warn("Attention, cannot return the length requested for subseq",1); } return $str;
}
seqdescriptionprevnextTop
sub seq {
  my $self=shift;
  my ($aa_start,$aa_end)=($self->aa_start,$self->aa_end);
  unless (($aa_start)&&($aa_end)) { # they must both exist
$self->warn("Not able to find start or end of the AminoAcid Range"); return (0); } my $translseq=$self->get_Translation->seq; return substr($translseq,$aa_start-1,$aa_end-$aa_start+1); # Note: it will return "undef" if the translation stops before the start
# of the aarange (because of upstream nonsense mutation creating STOP).
# For the same reason it would return uncomplete (up to the STOP) string
# if the stop happens in between aarange's start and stop
}
lengthdescriptionprevnextTop
sub length {
  my $self=shift;
  my $seq=$self->seq;
  my $length=length($seq);
  return $length;
}
labeldescriptionprevnextTop
sub label {
  my ($self,$position)=@_;
  my $translation=$self->get_Translation;
  my $origstart=$translation->coordinate_start; # preserve it
$translation->coordinate_start($self->start); # change it
my $label=$translation->label($position); $translation->coordinate_start($origstart); # restore it
return ($label);
}
positiondescriptionprevnextTop
sub position {
  my ($self,$label)=@_;
  my $translation=$self->get_Translation;
  my $origstart=$translation->coordinate_start; # preserve it
$translation->coordinate_start($self->start); # change it
my $position=$translation->position($label); $translation->coordinate_start($origstart); # restore it
return ($position);
}
aa_startdescriptionprevnextTop
sub aa_start {
  my $self=shift;
  my $aastart=$self->get_Translation->position($self->{'start'});
}
aa_enddescriptionprevnextTop
sub aa_end {
  my $self=shift;
  my $aastart=$self->get_Translation->position($self->{'end'});
}
dna_seqdescriptionprevnextTop
sub dna_seq {
  my $self=shift;
  my $startlabel=$self->start;
  my $endtripletlabel=$self->end;
  my $endlabel=$self->{'seq'}->label(3,$endtripletlabel,$self->strand);
  return ($self->labelsubseq($startlabel,undef,$endlabel));
}
cdna_seqdescriptionprevnextTop
sub cdna_seq {
  my $self=shift;
  my $startlabel=$self->start;
  my $endtripletlabel=$self->end;
  my $endlabel=$self->{'seq'}->label(3,$endtripletlabel,$self->strand);
  return ($self->get_Transcript->labelsubseq($startlabel,undef,$endlabel));
}

# this checks if the attached Transcript has a Gene object attached
}
genedescriptionprevnextTop
sub gene {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'gene'} = $value;
  }
  unless (exists $self->{'gene'}) {
    unless (exists $self->get_Transcript->{'gene'}) {
      return (0);
    } else {
      return ($self->get_Transcript->{'gene'});
    }
  } else {
    return $self->{'gene'};
  }
}

1;
}
General documentation
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _