Commit fec0136f authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Clean module names and VERSION var

parent 63666c11
#File output_checker.pm
#File CheckOutput.pm
package output_checker;
package CheckOutput;
sub translate{
......
......@@ -36,7 +36,7 @@ $ENV{'PATH'} .= ':/mnt/local/bin/'; # additional path for executable on the serv
#TODO: remove problematic char when "** FATAL ERROR **: Unrecognised symbol '0' (ascii:48) fi..."
my $Version = '4.0.0';
my $VERSION = '4.0.0';
my $uct = 15; # UpdateCacheThreshold: number of days before update
my $cachedir = '/scratch/cluster/monthly/t_coffee/ProtoGene_Cache'; # Cache directory
##### User settings ####################################
......@@ -82,7 +82,7 @@ GetOptions("msa|in=s" => \$msa, #Input sequences
);
$athome = 2 if ( $giga==1 );
if ( $version==1 ){
print "\n\tPROTOGENE : Bona-Fide Back Translation of Protein Multiple Sequence Alignments\n\tversion : $Version\n\n";
print "\n\tPROTOGENE : Bona-Fide Back Translation of Protein Multiple Sequence Alignments\n\tversion : $VERSION\n\n";
exit 0;
}
if ( $help==1 ){
......@@ -212,13 +212,13 @@ if ( $giga==1 ){
#Start main program with version # of programs and list original queries
print "\n\t Protogene\t$Version\t$date\n\n";
print "\n\t Protogene\t$VERSION\t$date\n\n";
open(my $EXONERATEISHERE, "$exonerate --version |");
my $IsExonerateHere = <$EXONERATEISHERE>;
close $EXONERATEISHERE;
print "\t $IsExonerateHere\n";
undef $IsExonerateHere;
undef $Version;
undef $VERSION;
for(my $m=0; $m<=$#original_names; $m++){
print "\t$original_names[$m]\n";
}
......
......@@ -9,9 +9,9 @@ runbla=`which runblast.pl`
echo 'history.txt'
read hist
echo 'loci_from_Exonerate.pm'
echo 'Exonerate.pm'
read loci
echo 'output_checker.pm'
echo 'CheckOutput.pm'
read output
echo 'installer.temp'
read instalTMP
......
......@@ -155,9 +155,9 @@ History of ProtoGene/PACMAN improvements:
0.95 - 24 oct 2005
Correct hash table variable define as semi-local, and not strictly as
local, in loci_from_Exonerate.pm because some value were kept between
local, in Exonerate.pm because some value were kept between
module executions due to misplaced brackets.
Clean loci_from_Exonerate.pm file and remove usage of strand, exonup
Clean Exonerate.pm file and remove usage of strand, exonup
list and genomic length because they are unnecessary here.
0.9 - 20 oct 2005
......
......@@ -137,14 +137,14 @@ mkdir tempOFtmp
sed -n -e '/#@@@@@@@ \DELIM1 @@@@@@@#/,/#@@@@@@@ \DELIM2 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/ProtoGene.pl
sed -n -e '/#@@@@@@@ \DELIM2 @@@@@@@#/,/#@@@@@@@ \DELIM3 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/webblast.pl
sed -n -e '/#@@@@@@@ \DELIM3 @@@@@@@#/,/#@@@@@@@ \DELIM4 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/runblast.pl
sed -n -e '/#@@@@@@@ \DELIM4 @@@@@@@#/,/#@@@@@@@ \DELIM5 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/loci_from_Exonerate.pm
sed -n -e '/#@@@@@@@ \DELIM5 @@@@@@@#/,/#@@@@@@@ \DELIM6 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/output_checker.pm
sed -n -e '/#@@@@@@@ \DELIM4 @@@@@@@#/,/#@@@@@@@ \DELIM5 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/Exonerate.pm
sed -n -e '/#@@@@@@@ \DELIM5 @@@@@@@#/,/#@@@@@@@ \DELIM6 @@@@@@@#/p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/CheckOutput.pm
sed -n -e '/#@@@@@@@ \DELIM6 @@@@@@@#/,$p' $0 | grep -v '@@@@@@@ DELIM' >tempOFtmp/history.txt
#Apply paths to files
chmod 555 tempOFtmp/ProtoGene.pl tempOFtmp/webblast.pl tempOFtmp/runblast.pl
chmod 444 tempOFtmp/loci_from_Exonerate.pm tempOFtmp/output_checker.pm tempOFtmp/history.txt
chmod 555 tempOFtmp/ProtoGene.pl tempOFtmp/webblast.pl tempOFtmp/runblast.pl
chmod 444 tempOFtmp/Exonerate.pm tempOFtmp/CheckOutput.pm tempOFtmp/history.txt
export protoCACHE
export protoLIB
......@@ -156,8 +156,8 @@ perl -i -pe "s{exonerate-1.0}{exonerate}" tempOFtmp/ProtoGene.pl #to deal with V
perl -i -pe "s{(my \\\$runblast = ')[^']*('.*)$}{\$1\$ENV{protoDIR}/runblast.pl\$2}" tempOFtmp/webblast.pl
mv -f tempOFtmp/loci_from_Exonerate.pm tempOFtmp/output_checker.pm tempOFtmp/history.txt $protoLIB
mv -f tempOFtmp/ProtoGene.pl tempOFtmp/webblast.pl tempOFtmp/runblast.pl $protoDIR
mv -f tempOFtmp/Exonerate.pm tempOFtmp/CheckOutput.pm tempOFtmp/history.txt $protoLIB
mv -f tempOFtmp/ProtoGene.pl tempOFtmp/webblast.pl tempOFtmp/runblast.pl $protoDIR
rm -Rf tempOFtmp/
unset protoCACHE
......
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