Bio::Variation SeqDiff
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Summary
Bio::Variation::SeqDiff - Container class for mutation/variant descriptions
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Bio::Tools::CodonTable
Inherit
Bio::Root::Root
Synopsis
  $seqDiff = Bio::Variation::SeqDiff->new (
-id => $M20132,
-alphabet => 'rna',
-gene_symbol => 'AR'
-chromosome => 'X',
-numbering => 'coding'
);
# get a DNAMutation object somehow
$seqDiff->add_Variant($dnamut);
print $seqDiff->sys_name(), "\n";
Description
SeqDiff stores Bio::Variation::VariantI object references and
descriptive information common to all changes in a sequence. Mutations
are understood to be any kind of sequence markers and are expected to
occur in the same chromosome. See Bio::Variation::VariantI for details.
The methods of SeqDiff are geared towards describing mutations in
human genes using gene-based coordinate system where 'A' of the
initiator codon has number 1 and the one before it -1. This is
according to conventions of human genetics.
There will be class Bio::Variation::Genotype to describe markers in
different chromosomes and diploid genototypes.
Classes implementing Bio::Variation::VariantI interface are
Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
Bio::Variation::AAChange. See Bio::Variation::VariantI,
Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
Bio::Variation::AAChange for more information.
Variant objects can be added using two ways: an array passed to the
constructor or as individual Variant objects with add_Variant
method.
Methods
newDescriptionCode
idDescriptionCode
sysnameDescriptionCode
trivnameDescriptionCode
chromosomeDescriptionCode
gene_symbolDescriptionCode
descriptionDescriptionCode
alphabetDescriptionCode
numberingDescriptionCode
offsetDescriptionCode
cds_startDescriptionCode
cds_endDescriptionCode
rna_offsetDescriptionCode
rna_idDescriptionCode
add_VariantDescriptionCode
each_VariantDescriptionCode
add_GeneDescriptionCode
each_GeneDescriptionCode
dna_oriDescriptionCode
dna_mutDescriptionCode
_set_dnamut
No description
Code
rna_oriDescriptionCode
rna_mutDescriptionCode
aa_oriDescriptionCode
aa_mutDescriptionCode
seqobjDescriptionCode
alignmentDescriptionCode
Methods description
newcode    nextTop
  Title   : new
Usage : $seqDiff = Bio::Variation::SeqDiff->new;
Function: generates a new Bio::Variation::SeqDiff
Returns : reference to a new object of class SeqDiff
Args :
idcodeprevnextTop
 Title   : id
Usage : $obj->id(H0001); $id = $obj->id();
Function:
Sets or returns the id of the seqDiff. Should be used to give the collection of variants a UID without semantic associations. Example : Returns : value of id, a scalar Args : newvalue (optional)
sysnamecodeprevnextTop
 Title   : sysname
Usage : $obj->sysname('5C>G'); $sysname = $obj->sysname();
Function:
Sets or returns the systematic name of the seqDiff. The name should follow the HUGO Mutation Database Initiative approved nomenclature. If called without first setting the value, will generate it from Bio::Variation::DNAMutation
objects attached.
Example : Returns : value of sysname, a scalar Args : newvalue (optional)
trivnamecodeprevnextTop
 Title   : trivname
Usage : $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname();
Function:
Sets or returns the trivial name of the seqDiff. The name should follow the HUGO Mutation Database Initiative approved nomenclature. If called without first setting the value, will generate it from Bio::Variation::AAChange
objects attached.
Example : Returns : value of trivname, a scalar Args : newvalue (optional)
chromosomecodeprevnextTop
 Title   : chromosome
Usage : $obj->chromosome('X'); $chromosome = $obj->chromosome();
Function:
Sets or returns the chromosome ("linkage group") of the seqDiff. Example : Returns : value of chromosome, a scalar Args : newvalue (optional)
gene_symbolcodeprevnextTop
 Title   : gene_symbol
Usage : $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol;
Function:
Sets or returns the gene symbol for the studied CDS. Example : Returns : value of gene_symbol, a scalar Args : newvalue (optional)
descriptioncodeprevnextTop
 Title   : description
Usage : $obj->description('short description'); $descr = $obj->description();
Function:
Sets or returns the short description of the seqDiff. Example : Returns : value of description, a scalar Args : newvalue (optional)
alphabetcodeprevnextTop
 Title   : alphabet
Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of primary reference sequence being one of
'dna', 'rna' or 'protein'. This is case sensitive.
Returns : a string either 'dna','rna','protein'. Args : none
numberingcodeprevnextTop
 Title   : numbering
Usage : $obj->numbering('coding'); $numbering = $obj->numbering();
Function:
Sets or returns the string giving the numbering schema used to describe the variants. Example : Returns : value of numbering, a scalar Args : newvalue (optional)
offsetcodeprevnextTop
 Title   : offset
Usage : $obj->offset(124); $offset = $obj->offset();
Function:
Sets or returns the offset from the beginning of the DNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. The cds_start should be 1 + offset. Example : Returns : value of offset, a scalar Args : newvalue (optional)
cds_startcodeprevnextTop
 Title   : cds_start
Usage : $obj->cds_start(123); $cds_start = $obj->cds_start();
Function:
Sets or returns the cds_start from the beginning of the DNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. Needs to be and is implemented as 1 + offset. Example : Returns : value of cds_start, a scalar Args : newvalue (optional)
cds_endcodeprevnextTop
 Title   : cds_end
Usage : $obj->cds_end(321); $cds_end = $obj->cds_end();
Function:
Sets or returns the position of the last nucleotitide of the termination codon. The coordinate system starts from cds_start. Example : Returns : value of cds_end, a scalar Args : newvalue (optional)
rna_offsetcodeprevnextTop
 Title   : rna_offset
Usage : $obj->rna_offset(124); $rna_offset = $obj->rna_offset();
Function:
Sets or returns the rna_offset from the beginning of the RNA sequence to the coordinate start used to describe variants. Typically the beginning of the coding region of the gene. Example : Returns : value of rna_offset, a scalar Args : newvalue (optional)
rna_idcodeprevnextTop
 Title   : rna_id
Usage : $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id();
Function:
Sets or returns the ID for original RNA sequence of the seqDiff. Example : Returns : value of rna_id, a scalar Args : newvalue (optional)
add_VariantcodeprevnextTop
 Title   : add_Variant
Usage : $obj->add_Variant($variant)
Function:
Pushes one Bio::Variation::Variant into the list of variants. At the same time, creates a link from the Variant to SeqDiff using its SeqDiff method. Example : Returns : 1 when succeeds, 0 for failure. Args : Variant object
each_VariantcodeprevnextTop
 Title   : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants. Example : Returns : list of Variants Args : none
add_GenecodeprevnextTop
 Title   : add_Gene
Usage : $obj->add_Gene($gene)
Function:
Pushes one Bio::LiveSeq::Gene into the list of genes.
Example : Returns : 1 when succeeds, 0 for failure. Args : Bio::LiveSeq::Gene object
See Bio::LiveSeq::Gene for more information.
each_GenecodeprevnextTop
 Title   : each_Gene
Usage : $obj->each_Gene();
Function:
Returns a list of Bio::LiveSeq::Genes.
Example : Returns : list of Genes Args : none
dna_oricodeprevnextTop
 Title   : dna_ori
Usage : $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori();
Function:
Sets or returns the original DNA sequence string of the seqDiff. Example : Returns : value of dna_ori, a scalar Args : newvalue (optional)
dna_mutcodeprevnextTop
 Title   : dna_mut
Usage : $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut();
Function:
Sets or returns the mutated DNA sequence of the seqDiff. If sequence has not been set generates it from the original sequence and DNA mutations. Example : Returns : value of dna_mut, a scalar Args : newvalue (optional)
rna_oricodeprevnextTop
 Title   : rna_ori
Usage : $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori();
Function:
Sets or returns the original RNA sequence of the seqDiff. Example : Returns : value of rna_ori, a scalar Args : newvalue (optional)
rna_mutcodeprevnextTop
 Title   : rna_mut
Usage : $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut();
Function:
Sets or returns the mutated RNA sequence of the seqDiff. Example : Returns : value of rna_mut, a scalar Args : newvalue (optional)
aa_oricodeprevnextTop
 Title   : aa_ori
Usage : $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori();
Function:
Sets or returns the original protein sequence of the seqDiff. Example : Returns : value of aa_ori, a scalar Args : newvalue (optional)
aa_mutcodeprevnextTop
 Title   : aa_mut
Usage : $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut();
Function:
Sets or returns the mutated protein sequence of the seqDiff. Example : Returns : value of aa_mut, a scalar Args : newvalue (optional)
seqobjcodeprevnextTop
 Title   : seqobj
Usage : $dnaobj = $obj->seqobj('dna_mut');
Function:
Returns the any original or mutated sequences as a Bio::PrimarySeq object. Example : Returns : Bio::PrimarySeq object for the requested sequence Args : string, method name for the sequence requested
See Bio::PrimarySeq for more information.
alignmentcodeprevnextTop
 Title   : alignment
Usage : $obj->alignment
Function:
Returns a pretty RNA/AA sequence alignment from linked objects. Under construction: Only simple coding region point mutations work. Example : Returns : Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id, $sysname, $trivname, $chr, $gene_symbol, 
       $desc, $alphabet, $numbering, $offset, $rna_offset, $rna_id, $cds_end,
       $dna_ori, $dna_mut, $rna_ori, $rna_mut, $aa_ori, $aa_mut
       #@variants, @genes
) = $self->_rearrange([qw(ID SYSNAME TRIVNAME CHR GENE_SYMBOL DESC ALPHABET NUMBERING OFFSET RNA_OFFSET RNA_ID CDS_END DNA_ORI DNA_MUT RNA_ORI AA_ORI AA_MUT )], @args); #my $make = $self->SUPER::_initialize(@args);
$id && $self->id($id); $sysname && $self->sysname($sysname); $trivname && $self->trivname($trivname); $chr && $self->chromosome($chr); $gene_symbol && $self->gene_symbol($chr); $desc && $self->description($desc); $alphabet && $self->alphabet($alphabet); $numbering && $self->numbering($numbering); $offset && $self->offset($offset); $rna_offset && $self->rna_offset($rna_offset); $rna_id && $self->rna_id($rna_id); $cds_end && $self->cds_end($cds_end); $dna_ori && $self->dna_ori($dna_ori); $dna_mut && $self->dna_mut($dna_mut); $rna_ori && $self->rna_ori($rna_ori); $rna_mut && $self->rna_mut($rna_mut); $aa_ori && $self->aa_ori ($aa_ori); $aa_mut && $self->aa_mut ($aa_mut); $self->{ 'variants' } = []; #@variants && push(@{$self->{'variants'}},@variants);
$self->{ 'genes' } = []; #@genes && push(@{$self->{'genes'}},@genes);
return $self; # success - we hope!
}
iddescriptionprevnextTop
sub id {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'id'} = $value;
  }
  else {
      return $self->{'id'};
  }
}
sysnamedescriptionprevnextTop
sub sysname {
    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'sysname'} = $value;
    }
    elsif (not defined $self->{'sysname'}) {

	my $sysname = ''; 
	my $c = 0;
	foreach my $mut ($self->each_Variant) {
	    if( $mut->isa('Bio::Variation::DNAMutation') ) {
		$c++;
		if ($c == 1 ) {
		    $sysname = $mut->sysname ;
		}
		else {
		    $sysname .= ";". $mut->sysname;
		}
	    }
	}
	$sysname  = "[". $sysname. "]" if $c > 1;
	$self->{'sysname'} = $sysname;
    }
    return $self->{'sysname'};
}
trivnamedescriptionprevnextTop
sub trivname {
    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'trivname'} = $value;
    }
    elsif (not defined $self->{'trivname'}) {
	
	my $trivname = ''; 
	my $c = 0;
	foreach my $mut ($self->each_Variant) {
	    if( $mut->isa('Bio::Variation::AAChange') ) {
		$c++;
		if ($c == 1 ) {
		    $trivname = $mut->trivname ;
		}
		else {
		    $trivname .= ";". $mut->trivname;
		}
	    }
	}
	$trivname  = "[". $trivname. "]" if $c > 1;
	$self->{'trivname'} = $trivname;
    }

  else {
      return $self->{'trivname'};
  }
}
chromosomedescriptionprevnextTop
sub chromosome {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'chromosome'} = $value;
  }
  else {
      return $self->{'chromosome'};
  }
}
gene_symboldescriptionprevnextTop
sub gene_symbol {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'gene_symbol'} = $value;
  }
  else {
      return $self->{'gene_symbol'};
  }
}
descriptiondescriptionprevnextTop
sub description {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'description'} = $value;
  }
  else {
      return $self->{'description'};
  }
}
alphabetdescriptionprevnextTop
sub alphabet {
   my ($self,$value) = @_;
   my %type = (dna => 1,
	       rna => 1,
	       protein => 1);
   if( defined $value ) {
       if ($type{$value}) {
	   $self->{'alphabet'} = $value;
       } else {
	   $self->throw("$value is not valid alphabet value!");
       }
   }
   return $self->{'alphabet'};
}
numberingdescriptionprevnextTop
sub numbering {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'numbering'} = $value;
  }
  else {
      return $self->{'numbering'};
  }
}
offsetdescriptionprevnextTop
sub offset {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'offset'} = $value;
  }
  elsif (not defined $self->{'offset'} ) {
      return $self->{'offset'} = 0;
  }
  else {
      return $self->{'offset'};
  }
}
cds_startdescriptionprevnextTop
sub cds_start {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'offset'} = $value - 1;
  }
  else {
      return $self->{'offset'} + 1;
  }
}
cds_enddescriptionprevnextTop
sub cds_end {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'cds_end'} = $value;
  }
  else {
      return $self->{'cds_end'};
      #$self->{'cds_end'} = CORE::length($self->SeqDiff->rna_ori)/3;
}
}
rna_offsetdescriptionprevnextTop
sub rna_offset {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'rna_offset'} = $value;
  }
  elsif (not defined $self->{'rna_offset'} ) {
      return $self->{'rna_offset'} = 0;
  }
  else {
      return $self->{'rna_offset'};
  }
}
rna_iddescriptionprevnextTop
sub rna_id {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'rna_id'} = $value;
  }
  else {
      return $self->{'rna_id'};
  }
}
add_VariantdescriptionprevnextTop
sub add_Variant {
  my ($self,$value) = @_;
  if (defined $value) {
      if( ! $value->isa('Bio::Variation::VariantI') ) {
	  $self->throw("Is not a VariantI complying  object but a [$self]");
	  return 0;
      }
      else {
	  push(@{$self->{'variants'}},$value);
	  $value->SeqDiff($self);
	  return 1;
      }
  }
  else {
      return 0;
  }
}
each_VariantdescriptionprevnextTop
sub each_Variant {
   my ($self,@args) = @_;
   
   return @{$self->{'variants'}};
}
add_GenedescriptionprevnextTop
sub add_Gene {
  my ($self,$value) = @_;
  if (defined $value) {
      if( ! $value->isa('Bio::LiveSeq::Gene') ) {
	  $value->throw("Is not a Bio::LiveSeq::Gene object but a  [$value]");
	  return 0;
      }
      else {
	  push(@{$self->{'genes'}},$value);
	  return 1;
      }
  }
  else {
      return 0;
  }
}
each_GenedescriptionprevnextTop
sub each_Gene {
   my ($self,@args) = @_;

   return @{$self->{'genes'}};
}
dna_oridescriptionprevnextTop
sub dna_ori {
  my ($self,$value) = @_;
  if (defined $value) {
      $self->{'dna_ori'} = $value;
  }
  else {
      return $self->{'dna_ori'};
  }
}
dna_mutdescriptionprevnextTop
sub dna_mut {
  my ($self,$value) = @_;
  if (defined $value) {
      $self->{'dna_mut'} = $value;
  }
  else {
      $self->_set_dnamut() unless $self->{'dna_mut'};
      return $self->{'dna_mut'};
  }
}
_set_dnamutdescriptionprevnextTop
sub _set_dnamut {
    my $self = shift;

    return unless $self->{'dna_ori'}  && $self->each_Variant;

    $self->{'dna_mut'} = $self->{'dna_ori'};
    foreach ($self->each_Variant) {
	next unless $_->isa('Bio::Variation::DNAMutation');
	next unless $_->isMutation;

	my ($s, $la, $le);
	#lies the mutation less than 25 bases after the start of sequence?
if ($_->start < 25) { $s = 0; $la = $_->start - 1; } else { $s = $_->start - 25; $la = 25; } #is the mutation an insertion?
$_->end($_->start) unless $_->allele_ori->seq; #does the mutation end greater than 25 bases before the end of
#sequence?
if (($_->end + 25) > length($self->{'dna_mut'})) { $le = length($self->{'dna_mut'}) - $_->end; } else { $le = 25; } $_->dnStreamSeq(substr($self->{'dna_mut'}, $s, $la)); $_->upStreamSeq(substr($self->{'dna_mut'}, $_->end, $le)); my $s_ori = $_->dnStreamSeq . $_->allele_ori->seq . $_->upStreamSeq; my $s_mut = $_->dnStreamSeq . $_->allele_mut->seq . $_->upStreamSeq; (my $str = $self->{'dna_mut'}) =~ s/$s_ori/$s_mut/; $self->{'dna_mut'} = $str; }
}
rna_oridescriptionprevnextTop
sub rna_ori {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'rna_ori'} = $value;
  }
  else {
      return $self->{'rna_ori'};
  }
}
rna_mutdescriptionprevnextTop
sub rna_mut {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'rna_mut'} = $value;
  }
  else {
      return $self->{'rna_mut'};
  }
}
aa_oridescriptionprevnextTop
sub aa_ori {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'aa_ori'} = $value;
  }
  else {
      return $self->{'aa_ori'};
  }
}
aa_mutdescriptionprevnextTop
sub aa_mut {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'aa_mut'} = $value;
  }
  else {
      return $self->{'aa_mut'};
  }
}
seqobjdescriptionprevnextTop
sub seqobj {
  my ($self,$value) = @_;
  my $out;
  my %valid_obj = 
      map {$_, 1} qw(dna_ori rna_ori aa_ori dna_mut rna_mut aa_mut);
  $valid_obj{$value} ||
      $self->throw("Sequence type '$value' is not a valid type (".
                  join(',', map "'$_'", sort keys %valid_obj) .") lowercase");
  my ($alphabet) = $value =~ /([^_]+)/;
  my $id =  $self->id;
  $id =  $self->rna_id if $self->rna_id;
  $alphabet = 'protein' if $alphabet eq 'aa';
  $out = Bio::PrimarySeq->new
      ( '-seq' => $self->{$value},
	'-display_id'  => $id,
	'-accession_number' => $self->id,
	'-alphabet' => $alphabet
	) if   $self->{$value} ;
  return $out;
}
alignmentdescriptionprevnextTop
sub alignment {
    my $self = shift;
    my (@entry, $text);

    my $maxflanklen = 12;

    foreach my $mut ($self->each_Variant) {
	if( $mut->isa('Bio::Variation::RNAChange') ) {

	    my $upflank = $mut->upStreamSeq;
	    my $dnflank = $mut->dnStreamSeq;
	    my $cposd = $mut->codon_pos;
	    my $rori = $mut->allele_ori->seq;
	    my $rmut =  $mut->allele_mut->seq;
	    my $rseqoriu = '';
	    my $rseqmutu = '';
	    my $rseqorid = '';
	    my $rseqmutd = '';
	    my $aaseqmutu = '';
	    my (@rseqori, @rseqmut );

	    #  point
if ($mut->DNAMutation->label =~ /point/) { if ($cposd == 1 ) { my $nt2d = substr($dnflank, 0, 2); push @rseqori, $rori. $nt2d; push @rseqmut, uc ($rmut). $nt2d; $dnflank = substr($dnflank, 2); } elsif ($cposd == 2) { my $ntu = chop $upflank; my $ntd = substr($dnflank, 0, 1); push @rseqori, $ntu. $rori. $ntd; push @rseqmut, $ntu. uc ($rmut). $ntd; $dnflank = substr($dnflank, 1); } elsif ($cposd == 3) { my $ntu1 = chop $upflank; my $ntu2 = chop $upflank; push (@rseqori, $ntu2. $ntu1. $rori); push (@rseqmut, $ntu2. $ntu1. uc $rmut); } } #deletion
elsif ($mut->DNAMutation->label =~ /deletion/) { if ($cposd == 2 ) { $rseqorid = chop $upflank; $rseqmutd = $rseqorid; } for (my $i=1; $i<=$mut->length; $i++) { my $ntd .= substr($mut->allele_ori, $i-1, 1); $rseqorid .= $ntd; if (length($rseqorid) == 3 ) { push (@rseqori, $rseqorid); push (@rseqmut, " "); $rseqorid = ''; } } if ($rseqorid) { $rseqorid .= substr($dnflank, 0, 3-$rseqorid); push (@rseqori, $rseqorid); push (@rseqmut, " "); $dnflank = substr($dnflank,3-$rseqorid); } } $upflank = reverse $upflank; # loop throught the flanks
for (my $i=1; $i<=length($dnflank); $i++) { last if $i > $maxflanklen; my $ntd .= substr($dnflank, $i-1, 1); my $ntu .= substr($upflank, $i-1, 1); $rseqmutd .= $ntd; $rseqorid .= $ntd; $rseqmutu = $ntu. $rseqmutu; $rseqoriu = $ntu. $rseqoriu; if (length($rseqorid) == 3 and length($rseqorid) == 3) { push (@rseqori, $rseqorid); push (@rseqmut, $rseqmutd); $rseqorid = $rseqmutd =''; } if (length($rseqoriu) == 3 and length($rseqoriu) == 3) { unshift (@rseqori, $rseqoriu); unshift (@rseqmut, $rseqmutu); $rseqoriu = $rseqmutu =''; } #print "|i=$i, $cposd, $rseqmutd, $rseqorid\n";
#print "|i=$i, $cposu, $rseqmutu, $rseqoriu\n\n";
} push (@rseqori, $rseqorid); unshift (@rseqori, $rseqoriu); push (@rseqmut, $rseqmutd); unshift (@rseqmut, $rseqmutu); return unless $mut->AAChange; #translate
my $tr = Bio::Tools::CodonTable->new('-id' => $mut->codon_table); my $apos = $mut->AAChange->start; my $aposmax = CORE::length($self->aa_ori); #terminator codon no
my $rseqori; my $rseqmut; my $aaseqori; my $aaseqmut = ""; for (my $i = 0; $i <= $#rseqori; $i++) { my $a = ''; $a = $tr->translate($rseqori[$i]) if length($rseqori[$i]) == 3; if (length($a) != 1 or $apos - ( $maxflanklen/2 -1) + $i < 1 or
$apos - ( $maxflanklen/2 -1) + $i > $aposmax ) { $aaseqori .= " "; } else { $aaseqori .= " ". $a. " "; } my $b = ''; if (length($rseqmut[$i]) == 3) { if ($rseqmut[$i] eq ' ') { $b = "_"; } else { $b = $tr->translate($rseqmut[$i]); } } if (( $b ne $a and length($b) == 1 and $apos - ( $maxflanklen/2 -1) + $i >= 1 ) or
(
$apos - ( $maxflanklen/2 -1) + $i >= $aposmax and $mut->label =~ 'termination') ) { $aaseqmut .= " ". $b. " "; } else { $aaseqmut .= " "; } if ($i == 0 and length($rseqori[$i]) != 3) { my $l = 3 - length($rseqori[$i]); $rseqori[$i] = (" " x $l). $rseqori[$i]; $rseqmut[$i] = (" " x $l). $rseqmut[$i]; } $rseqori .= $rseqori[$i]. " " if $rseqori[$i] ne ''; $rseqmut .= $rseqmut[$i]. " " if $rseqmut[$i] ne ''; } # collect the results
push (@entry, "\n" ); $text = " ". $aaseqmut; push (@entry, $text ); $text = "Variant : ". $rseqmut; push (@entry, $text ); $text = "Reference: ". $rseqori; push (@entry, $text ); $text = " ". $aaseqori; push (@entry, $text ); push (@entry, "\n" ); } } my $res; foreach my $line (@entry) { $res .= "$line\n"; } return $res; } 1;
}
General documentation
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 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 - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Eckhard Lehmann, ecky@e-lehmann.de
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _