Merge branch 'release-0.8.5c-beta'

Author: brainfood

norm_scripts/get_chr_stats.pl

@@ -116,7 +116,7 @@
         $file = "$LOC/$line/EIJ/Unique/$line.filtered_u.numchr_count.txt";
     }
     foreach my $key (sort {&cmpChrs($a,$b)} keys %CHR){
-	my $find = `grep -w '$key' $file`;
+	my $find = `grep -w '^$key' $file`;
 	my $count = "0.00";
 	if ($find !~ /^$/){
 	    my @f = split(/\t/,$find);

norm_scripts/run_normalization

@@ -70,7 +70,7 @@ OPTIONS:
 
 for(my $i=0; $i<@ARGV; $i++) {
     if ($ARGV[$i] eq '-v'){
-	die "\nPORT v0.8.5b-beta\n\n";
+	die "\nPORT v0.8.5c-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 v0.8.5b-beta\n";
+print LOG "\nPORT v0.8.5c-beta\n";
 my $default_input = $input;
 #$default_input = `cat $shdir/runall_normalization.sh`;
 $default_input =~ s/perl\ //g;
@@ -2692,12 +2692,12 @@
 	    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";
                 print LOG "$exp_num_reads\n";
-                print LOG "See \"$exp_file\" \nand modify the list of sample directories (\"$sample_dir\") accordingly to get more reads.\n\n";
+                print LOG "See \"$s_dir/GENE/expected_num_reads_gnorm.txt\" \nand modify the list of sample directories (\"$sample_dir\") accordingly to get more reads.\n\n";
                 print LOG "(2) High Expressers\n";
 		my @highfiles = glob("$s_dir/GENE/percent_high_expresser_gene*txt");
 		my $highcnt = 0;

template_v0.8.5.cfg

@@ -1,5 +1,5 @@
 
-# config file for [PORT - RNA-Seq Normalization & Quantification] (v0.8.5b-beta)
+# config file for [PORT - RNA-Seq Normalization & Quantification] (v0.8.5c-beta)
 
 ######################################################################################################################