Commit b36694b4 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Small path fixes + remove most stderr debug outputs

parent fbded075
...@@ -57,7 +57,7 @@ sub parser{ ...@@ -57,7 +57,7 @@ sub parser{
} }
} }
close $MAP; close $MAP;
print "[@cdsUp]\n" if ( $debug ); print {*STDERR} "[@cdsUp]\n" if ( $debug );
my $drap = 0; my $drap = 0;
...@@ -72,11 +72,11 @@ sub parser{ ...@@ -72,11 +72,11 @@ sub parser{
if ( $drap==3 && $matched_symbol =~ /^[\+\-]$/ ){ if ( $drap==3 && $matched_symbol =~ /^[\+\-]$/ ){
$drap = 0; $drap = 0;
$locus = 0; $locus = 0;
print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug); print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
} }
elsif ( $matched_symbol =~ /^[\+\-]$/ ){ elsif ( $matched_symbol =~ /^[\+\-]$/ ){
$drap++; $drap++;
print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug); print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
} }
# elsif ( $matched_symbol =~ /[ \|\.\!\:]/ && substr($Genom,$i,1) !~ /[\{\}\.a-z\-]/ ){ # elsif ( $matched_symbol =~ /[ \|\.\!\:]/ && substr($Genom,$i,1) !~ /[\{\}\.a-z\-]/ ){
elsif ( $matched_symbol =~ /[ \|\.\!\:\#]/ && substr($Genom, $i, 1) !~ /[\{\}\.a-z]/ ){ elsif ( $matched_symbol =~ /[ \|\.\!\:\#]/ && substr($Genom, $i, 1) !~ /[\{\}\.a-z]/ ){
...@@ -108,16 +108,16 @@ sub parser{ ...@@ -108,16 +108,16 @@ sub parser{
} }
my $shift = ''; my $shift = '';
$shift = "\t$frameIntron" if ( $frameIntron>0 ); $shift = "\t$frameIntron" if ( $frameIntron>0 );
print $line, "$shift\n" if ($debug); print {*STDERR} $line, "$shift\n" if ($debug);
$locus++; $locus++;
} }
elsif ( $matched_symbol =~ /\{/ ){ elsif ( $matched_symbol =~ /\{/ ){
print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug); print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
$frameIntron = -1; $frameIntron = -1;
$accolade++; $accolade++;
} }
else{ else{
print $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug); print {*STDERR} $matched_symbol, substr($Genom, $i, 1), "\t", substr($Query, $i, 1), "\n" if ($debug);
$lieu++ if ( substr($Query, $i, 1) =~ /U/ ); $lieu++ if ( substr($Query, $i, 1) =~ /U/ );
if ( substr($Query, $i, 1) =~ /\}/ ){ if ( substr($Query, $i, 1) =~ /\}/ ){
if ( $frameIntron==1 ){ if ( $frameIntron==1 ){
......
...@@ -68,7 +68,7 @@ sub Html { ...@@ -68,7 +68,7 @@ sub Html {
open (my $CDSP, '<', "$file") or die "\tCannot open '$file'\n"; open (my $CDSP, '<', "$file") or die "\tCannot open '$file'\n";
open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n"; open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n";
print {$CDSHTML} &htmlHeader($file); print {$CDSHTML} htmlHeader($file);
{ {
my $isOdd = 'odd'; my $isOdd = 'odd';
my $isSubOdd = 'odd'; my $isSubOdd = 'odd';
...@@ -162,7 +162,7 @@ sub Html { ...@@ -162,7 +162,7 @@ sub Html {
sub htmlHeader { sub htmlHeader {
my ($jobName) = @_; my ($jobName) = @_;
$jobName =~ s{^.*/([^\/]+?)\.cdsP$}{$1}; $jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
my $css = ''; my $css = '';
for my $style ( keys(%css) ){ for my $style ( keys(%css) ){
......
...@@ -198,7 +198,7 @@ sub Html { ...@@ -198,7 +198,7 @@ sub Html {
open (my $CDSP, '<', "$file") or die "\tCannot open '$file'\n"; open (my $CDSP, '<', "$file") or die "\tCannot open '$file'\n";
open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n"; open (my $CDSHTML, '>', "$file.html") or die "\tCannot create in '$file.html'\n";
print {$CDSHTML} &htmlHeader($file); print {$CDSHTML} htmlHeader($file);
{ {
my $isOdd = 'odd'; my $isOdd = 'odd';
my $isSubOdd = 'odd'; my $isSubOdd = 'odd';
...@@ -329,7 +329,7 @@ sub Html { ...@@ -329,7 +329,7 @@ sub Html {
sub htmlHeader { sub htmlHeader {
my ($jobName) = @_; my ($jobName) = @_;
$jobName =~ s{^.*/([^\/]+?)\.cdsP$}{$1}; $jobName =~ s{^.*?([^\/]+?)\.cdsP$}{$1};
my $css = ''; my $css = '';
for my $style ( keys(%css) ){ for my $style ( keys(%css) ){
......
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