Merge branch 'feature'

itmat · Mar 8, 2018 · 7709688 · 7709688
2 parents 6c624bb + df6e1cd
commit 7709688
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Showing 9 changed files with 17 additions and 17 deletions.
diff --git a/norm_scripts/get_master_list_of_exons.pl b/norm_scripts/get_master_list_of_exons.pl
@@ -359,11 +359,11 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])
-	(?: V?I{0,3} | I[VX])$/ix;
+	(?: V?I{0,3} | I[VX])$/ix);
 }
 
 

diff --git a/norm_scripts/get_master_list_of_genes.pl b/norm_scripts/get_master_list_of_genes.pl
@@ -368,10 +368,10 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])
-                 (?: V?I{0,3} | I[VX])$/ix;
+                 (?: V?I{0,3} | I[VX])$/ix);
 }
 
diff --git a/norm_scripts/get_master_list_of_intergenic_regions.pl b/norm_scripts/get_master_list_of_intergenic_regions.pl
@@ -621,11 +621,11 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])
-	(?: V?I{0,3} | I[VX])$/ix;
+	(?: V?I{0,3} | I[VX])$/ix);
 }
 
 sub uniq {

diff --git a/norm_scripts/get_master_list_of_introns.pl b/norm_scripts/get_master_list_of_introns.pl
@@ -337,9 +337,9 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
 	(?: D?C{0,3} | C[DM])
 	(?: L?X{0,3} | X[LC])
-	(?: V?I{0,3} | I[VX])$/ix;
+	(?: V?I{0,3} | I[VX])$/ix);
 }
diff --git a/norm_scripts/quantify_exons_introns.pl b/norm_scripts/quantify_exons_introns.pl
@@ -1646,11 +1646,11 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])
-                 (?: V?I{0,3} | I[VX])$/ix;
+                 (?: V?I{0,3} | I[VX])$/ix);
 }
 
 

diff --git a/norm_scripts/quantify_intergenic_regions.pl b/norm_scripts/quantify_intergenic_regions.pl
@@ -605,11 +605,11 @@ ($)
 }
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
 	$arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])
-                 (?: V?I{0,3} | I[VX])$/ix;
+                 (?: V?I{0,3} | I[VX])$/ix);
 }
 
 

diff --git a/norm_scripts/quantify_introns.pl b/norm_scripts/quantify_introns.pl
@@ -362,11 +362,11 @@ ($)
 
 sub isroman($) {
     my $arg = shift;
-    return $arg ne '' and
+    return ($arg ne '' and
         $arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])
-                 (?: V?I{0,3} | I[VX])$/ix;
+                 (?: V?I{0,3} | I[VX])$/ix);
 }
 
 

diff --git a/norm_scripts/rum-2.0.5_05/lib/RUM/Common.pm b/norm_scripts/rum-2.0.5_05/lib/RUM/Common.pm
@@ -97,11 +97,11 @@ 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 '' and
         $arg =~ /^(?: M{0,3})
                  (?: D?C{0,3} | C[DM])
                  (?: L?X{0,3} | X[LC])
-                 (?: V?I{0,3} | I[VX])$/ix;
+                 (?: V?I{0,3} | I[VX])$/ix);
 }
 
 =item arabic(N)

diff --git a/norm_scripts/runall_normalization.pl b/norm_scripts/runall_normalization.pl
@@ -2692,7 +2692,7 @@
 	    print LOG "Check the following before proceeding:\n\n";
 
 	    if ($GNORM eq "true"){
-                $exp_num_reads = `grep -A 3 Expected $s_dir/GENE/expected_num_reads_gnorm.txt"; | grep -A 3 estimate`;
+                $exp_num_reads = `grep -A 3 Expected $s_dir/GENE/expected_num_reads_gnorm.txt" | grep -A 3 estimate`;
                 chomp($exp_num_reads);
                 print LOG "\n[Gene Normalization]\n";
                 print LOG "(1) Number of reads\n";