Raw content of Bio::Variation::SeqDiff
<![CDATA[# $Id: SeqDiff.pm,v 1.16 2002/10/22 07:38:49 lapp Exp $
# bioperl module for Bio::Variation::SeqDiff
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
# cds_end definition?
=head1 NAME
Bio::Variation::SeqDiff - Container class for mutation/variant descriptions
=head1 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";
=head1 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 L<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 L<Bio::Variation::VariantI>,
L<Bio::Variation::DNAMutation>, L<Bio::Variation::RNAChange>, and
L<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.
=head1 FEEDBACK
=head2 Mailing Lists
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://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=head1 CONTRIBUTORS
Eckhard Lehmann, ecky@e-lehmann.de
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Variation::SeqDiff;
my $VERSION=1.0;
use strict;
use vars qw($VERSION @ISA);
use Bio::Root::Root;
use Bio::Tools::CodonTable;
use Bio::PrimarySeq;
@ISA = qw( Bio::Root::Root );
=head2 new
Title : new
Usage : $seqDiff = Bio::Variation::SeqDiff->new;
Function: generates a new Bio::Variation::SeqDiff
Returns : reference to a new object of class SeqDiff
Args :
=cut
sub new {
my($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!
}
=head2 id
Title : id
Usage : $obj->id(H0001); $id = $obj->id();
Function:
Sets or returns the id of the seqDiff.
Should be used to give the collection of variants a UID
without semantic associations.
Example :
Returns : value of id, a scalar
Args : newvalue (optional)
=cut
sub id {
my ($self,$value) = @_;
if (defined $value) {
$self->{'id'} = $value;
}
# unless (exists $self->{'id'}) {
# return "undefined";
# }
else {
return $self->{'id'};
}
}
=head2 sysname
Title : sysname
Usage : $obj->sysname('5C>G'); $sysname = $obj->sysname();
Function:
Sets or returns the systematic name of the seqDiff. The
name should follow the HUGO Mutation Database Initiative
approved nomenclature. If called without first setting the
value, will generate it from L<Bio::Variation::DNAMutation>
objects attached.
Example :
Returns : value of sysname, a scalar
Args : newvalue (optional)
=cut
sub sysname {
my ($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'};
}
=head2 trivname
Title : trivname
Usage : $obj->trivname('[A2G;T56G]'); $trivname = $obj->trivname();
Function:
Sets or returns the trivial name of the seqDiff.
The name should follow the HUGO Mutation Database Initiative
approved nomenclature. If called without first setting the
value, will generate it from L<Bio::Variation::AAChange>
objects attached.
Example :
Returns : value of trivname, a scalar
Args : newvalue (optional)
=cut
sub trivname {
my ($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'};
}
}
=head2 chromosome
Title : chromosome
Usage : $obj->chromosome('X'); $chromosome = $obj->chromosome();
Function:
Sets or returns the chromosome ("linkage group") of the seqDiff.
Example :
Returns : value of chromosome, a scalar
Args : newvalue (optional)
=cut
sub chromosome {
my ($self,$value) = @_;
if (defined $value) {
$self->{'chromosome'} = $value;
}
else {
return $self->{'chromosome'};
}
}
=head2 gene_symbol
Title : gene_symbol
Usage : $obj->gene_symbol('FOS'); $gene_symbol = $obj->gene_symbol;
Function:
Sets or returns the gene symbol for the studied CDS.
Example :
Returns : value of gene_symbol, a scalar
Args : newvalue (optional)
=cut
sub gene_symbol {
my ($self,$value) = @_;
if (defined $value) {
$self->{'gene_symbol'} = $value;
}
else {
return $self->{'gene_symbol'};
}
}
=head2 description
Title : description
Usage : $obj->description('short description'); $descr = $obj->description();
Function:
Sets or returns the short description of the seqDiff.
Example :
Returns : value of description, a scalar
Args : newvalue (optional)
=cut
sub description {
my ($self,$value) = @_;
if (defined $value) {
$self->{'description'} = $value;
}
else {
return $self->{'description'};
}
}
=head2 alphabet
Title : alphabet
Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of primary reference sequence being one of
'dna', 'rna' or 'protein'. This is case sensitive.
Returns : a string either 'dna','rna','protein'.
Args : none
=cut
sub alphabet {
my ($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'};
}
=head2 numbering
Title : numbering
Usage : $obj->numbering('coding'); $numbering = $obj->numbering();
Function:
Sets or returns the string giving the numbering schema used
to describe the variants.
Example :
Returns : value of numbering, a scalar
Args : newvalue (optional)
=cut
sub numbering {
my ($self,$value) = @_;
if (defined $value) {
$self->{'numbering'} = $value;
}
else {
return $self->{'numbering'};
}
}
=head2 offset
Title : offset
Usage : $obj->offset(124); $offset = $obj->offset();
Function:
Sets or returns the offset from the beginning of the DNA sequence
to the coordinate start used to describe variants. Typically
the beginning of the coding region of the gene.
The cds_start should be 1 + offset.
Example :
Returns : value of offset, a scalar
Args : newvalue (optional)
=cut
sub offset {
my ($self,$value) = @_;
if (defined $value) {
$self->{'offset'} = $value;
}
elsif (not defined $self->{'offset'} ) {
return $self->{'offset'} = 0;
}
else {
return $self->{'offset'};
}
}
=head2 cds_start
Title : cds_start
Usage : $obj->cds_start(123); $cds_start = $obj->cds_start();
Function:
Sets or returns the cds_start from the beginning of the DNA
sequence to the coordinate start used to describe
variants. Typically the beginning of the coding region of
the gene. Needs to be and is implemented as 1 + offset.
Example :
Returns : value of cds_start, a scalar
Args : newvalue (optional)
=cut
sub cds_start {
my ($self,$value) = @_;
if (defined $value) {
$self->{'offset'} = $value - 1;
}
else {
return $self->{'offset'} + 1;
}
}
=head2 cds_end
Title : cds_end
Usage : $obj->cds_end(321); $cds_end = $obj->cds_end();
Function:
Sets or returns the position of the last nucleotitide of the
termination codon. The coordinate system starts from cds_start.
Example :
Returns : value of cds_end, a scalar
Args : newvalue (optional)
=cut
sub cds_end {
my ($self,$value) = @_;
if (defined $value) {
$self->{'cds_end'} = $value;
}
else {
return $self->{'cds_end'};
#$self->{'cds_end'} = CORE::length($self->SeqDiff->rna_ori)/3;
}
}
=head2 rna_offset
Title : rna_offset
Usage : $obj->rna_offset(124); $rna_offset = $obj->rna_offset();
Function:
Sets or returns the rna_offset from the beginning of the RNA sequence
to the coordinate start used to describe variants. Typically
the beginning of the coding region of the gene.
Example :
Returns : value of rna_offset, a scalar
Args : newvalue (optional)
=cut
sub rna_offset {
my ($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'};
}
}
=head2 rna_id
Title : rna_id
Usage : $obj->rna_id('transcript#3'); $rna_id = $obj->rna_id();
Function:
Sets or returns the ID for original RNA sequence of the seqDiff.
Example :
Returns : value of rna_id, a scalar
Args : newvalue (optional)
=cut
sub rna_id {
my ($self,$value) = @_;
if (defined $value) {
$self->{'rna_id'} = $value;
}
else {
return $self->{'rna_id'};
}
}
=head2 add_Variant
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
=cut
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;
}
}
=head2 each_Variant
Title : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants.
Example :
Returns : list of Variants
Args : none
=cut
sub each_Variant{
my ($self,@args) = @_;
return @{$self->{'variants'}};
}
=head2 add_Gene
Title : add_Gene
Usage : $obj->add_Gene($gene)
Function:
Pushes one L<Bio::LiveSeq::Gene> into the list of genes.
Example :
Returns : 1 when succeeds, 0 for failure.
Args : Bio::LiveSeq::Gene object
See L<Bio::LiveSeq::Gene> for more information.
=cut
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;
}
}
=head2 each_Gene
Title : each_Gene
Usage : $obj->each_Gene();
Function:
Returns a list of L<Bio::LiveSeq::Gene>s.
Example :
Returns : list of Genes
Args : none
=cut
sub each_Gene{
my ($self,@args) = @_;
return @{$self->{'genes'}};
}
=head2 dna_ori
Title : dna_ori
Usage : $obj->dna_ori('atgctgctgctgct'); $dna_ori = $obj->dna_ori();
Function:
Sets or returns the original DNA sequence string of the seqDiff.
Example :
Returns : value of dna_ori, a scalar
Args : newvalue (optional)
=cut
sub dna_ori {
my ($self,$value) = @_;
if (defined $value) {
$self->{'dna_ori'} = $value;
}
else {
return $self->{'dna_ori'};
}
}
=head2 dna_mut
Title : dna_mut
Usage : $obj->dna_mut('atgctggtgctgct'); $dna_mut = $obj->dna_mut();
Function:
Sets or returns the mutated DNA sequence of the seqDiff.
If sequence has not been set generates it from the
original sequence and DNA mutations.
Example :
Returns : value of dna_mut, a scalar
Args : newvalue (optional)
=cut
sub dna_mut {
my ($self,$value) = @_;
if (defined $value) {
$self->{'dna_mut'} = $value;
}
else {
$self->_set_dnamut() unless $self->{'dna_mut'};
return $self->{'dna_mut'};
}
}
sub _set_dnamut {
my $self = shift;
return undef 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;
}
}
=head2 rna_ori
Title : rna_ori
Usage : $obj->rna_ori('atgctgctgctgct'); $rna_ori = $obj->rna_ori();
Function:
Sets or returns the original RNA sequence of the seqDiff.
Example :
Returns : value of rna_ori, a scalar
Args : newvalue (optional)
=cut
sub rna_ori {
my ($self,$value) = @_;
if (defined $value) {
$self->{'rna_ori'} = $value;
}
else {
return $self->{'rna_ori'};
}
}
=head2 rna_mut
Title : rna_mut
Usage : $obj->rna_mut('atgctggtgctgct'); $rna_mut = $obj->rna_mut();
Function:
Sets or returns the mutated RNA sequence of the seqDiff.
Example :
Returns : value of rna_mut, a scalar
Args : newvalue (optional)
=cut
sub rna_mut {
my ($self,$value) = @_;
if (defined $value) {
$self->{'rna_mut'} = $value;
}
else {
return $self->{'rna_mut'};
}
}
=head2 aa_ori
Title : aa_ori
Usage : $obj->aa_ori('MAGVLL*'); $aa_ori = $obj->aa_ori();
Function:
Sets or returns the original protein sequence of the seqDiff.
Example :
Returns : value of aa_ori, a scalar
Args : newvalue (optional)
=cut
sub aa_ori {
my ($self,$value) = @_;
if (defined $value) {
$self->{'aa_ori'} = $value;
}
else {
return $self->{'aa_ori'};
}
}
=head2 aa_mut
Title : aa_mut
Usage : $obj->aa_mut('MA*'); $aa_mut = $obj->aa_mut();
Function:
Sets or returns the mutated protein sequence of the seqDiff.
Example :
Returns : value of aa_mut, a scalar
Args : newvalue (optional)
=cut
sub aa_mut {
my ($self,$value) = @_;
if (defined $value) {
$self->{'aa_mut'} = $value;
}
else {
return $self->{'aa_mut'};
}
}
=head2 seqobj
Title : seqobj
Usage : $dnaobj = $obj->seqobj('dna_mut');
Function:
Returns the any original or mutated sequences as a
Bio::PrimarySeq object.
Example :
Returns : Bio::PrimarySeq object for the requested sequence
Args : string, method name for the sequence requested
See L<Bio::PrimarySeq> for more information.
=cut
sub seqobj {
my ($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;
}
=head2 alignment
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
=cut
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 = new Bio::Tools::CodonTable ('-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;
]]>