Merge branch 'feature' into develop for minor bug fixes.

itmat · May 11, 2018 · 09a5962 · 09a5962
2 parents 563568d + 79554a1
commit 09a5962
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/norm_scripts/get_chr_stats.pl b/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);

diff --git a/norm_scripts/runall_normalization.pl b/norm_scripts/runall_normalization.pl
@@ -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;