Commit 7a874457 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Allow revtrans to be a boolean or a string option (for tcoffee web server)

parent 9d4eddec
......@@ -55,7 +55,7 @@ my $blast_param = { 'evalue' => 0.05,
###################################################
my $VERSION = '4.2.0';
my $VERSION = '4.2.1';
my $webblast_exe = '/mnt/common/share/ProtoGene/webblast.pl';
my $blast_exe = 'blastall'; # Or wu-blastall for Wu-BLAST; for local blast usage
......@@ -67,7 +67,7 @@ my ($msa, $revtrans, $pep, $hideBOJ, $run_name, $template, $lim, $cache) = ('',
my ($debug, $tmp) = (0, 0);
my ($db, $species, $local, $giga) = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0);
my %opts = ('msa|in=s' => \$msa, # Input sequences
'revtrans' => \$revtrans, # Use to reverse-translate sequences with no match
'revtrans:s' => \$revtrans, # Use to reverse-translate sequences with no match
'pep' => \$pep, # Add the original peptide query beneath the related CDS seq
'hideBOJ' => \$hideBOJ, # Hide BOJ output
'run_name=s' => \$run_name, # Use another name, instead of input seq name, for result files
......@@ -90,6 +90,7 @@ my %opts = ('msa|in=s' => \$msa, # Input sequences
'tmp' => \$tmp, # To keep traces of fake intermediate files like fake xml from NCBI, fake aln, ...
);
my $test_option_values = Getopt::Long::GetOptions(%opts);
$revtrans = 1 if ( $revtrans eq '' ); # Allow revtrans to be a boolean or a string option (for tcoffee web server)
################## Short help message
......@@ -1433,7 +1434,7 @@ sub revtransBuilding{
$readyname =~ s{ +}{ }g;
print OUT "$readyname\n";
if ( $revtrans==1 ){
if ( $revtrans ){
my $final_seq = '';
for(my $w=0; $w < length($original_seq[$order]); $w++){
my $aa = substr($original_seq[$order], $w, 1);
......
......@@ -4,6 +4,9 @@
#Author: Sebastien Moretti
#E-mail: moretti.sebastien [AT] gmail.com
#
4.2.1
Fix for revtrans option that cannot be strictly boolean for the new
Tcoffee web server
4.2.0
Switch to exonerate 2.2.0
......
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