Merge branch 'release-0.8.5e-beta'

Author: brainfood

norm_scripts/get_master_list_of_exons.pl

@@ -359,7 +359,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])

norm_scripts/get_master_list_of_genes.pl

@@ -368,7 +368,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])

norm_scripts/get_master_list_of_intergenic_regions.pl

@@ -621,7 +621,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])

norm_scripts/get_master_list_of_introns.pl

@@ -337,7 +337,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])

norm_scripts/quantify_exons_introns.pl

@@ -1646,7 +1646,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])

norm_scripts/quantify_intergenic_regions.pl

@@ -605,7 +605,7 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])

norm_scripts/quantify_introns.pl

@@ -362,7 +362,7 @@ ($)
 
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
         $arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])

norm_scripts/rum-2.0.5_05/lib/RUM/Common.pm

@@ -97,7 +97,7 @@ Return a true value if N is a roman numeral, false otherwise.
 =cut
 sub isroman($) {
     my $arg = shift;
-    return ($arg ne '' and
+    return ($arg ne '' &&
         $arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])

norm_scripts/run_normalization

@@ -70,7 +70,7 @@ OPTIONS:
 
 for(my $i=0; $i<@ARGV; $i++) {
     if ($ARGV[$i] eq '-v'){
-	die "\nPORT v0.8.5d-beta\n\n";
+	die "\nPORT v0.8.5e-beta\n\n";
     }
 }
 for(my $i=0; $i<@ARGV; $i++) {

norm_scripts/runall_normalization.pl

@@ -612,7 +612,7 @@
     }
 }
 open(LOG, ">>$logfile");
-print LOG "\nPORT v0.8.5d-beta\n";
+print LOG "\nPORT v0.8.5e-beta\n";
 my $default_input = $input;
 #$default_input = `cat $shdir/runall_normalization.sh`;
 $default_input =~ s/perl\ //g;