Commit 3de29348 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

If * is in the original sequence no need to switch ---

parent ecb9cedd
......@@ -1274,6 +1274,9 @@ sub buildCDSseq{
my $locus = 0;
for(my $z=0; $z<=length($input_seq); $z++){
if ( $z==length($input_seq) ){
if ( $input_seq =~ /\*$/ ){ # If * is in the original sequence no need to switch ---
$cdsSeq =~ s{\-\-\-$}{};
}
$locus++;
if ( exists($POSITIONS{$locus}) && ($POSITIONS{$locus} eq 'TAA' || $POSITIONS{$locus} eq 'TAG' || $POSITIONS{$locus} eq 'TGA') ){
$cdsSeq .= $POSITIONS{$locus};
......@@ -1437,7 +1440,7 @@ sub revtransBuilding{
$final_seq = $final_seq.reverse_trad($aa);
}
$readyname =~ s{_G_$NTstatus _S_ $BLASTstatus }{_G_revtrans };
my $CDSreformatedSeq = $final_seq."---\n"; #FIXME: For stop codon ???
my $CDSreformatedSeq = $final_seq."---\n"; #FIXME For stop codon ???
$CDSreformatedSeq =~ s{([^\n]{60})}{$1\n}g;
chomp $CDSreformatedSeq if ( $CDSreformatedSeq =~ /\n+$/ );
print CDS "$readyname\n$CDSreformatedSeq";
......
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