diff --git a/norm_scripts/get_chr_stats.pl b/norm_scripts/get_chr_stats.pl index 05fb71b..3652147 100644 --- 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/run_normalization b/norm_scripts/run_normalization index fa239b1..c898a55 100755 --- a/norm_scripts/run_normalization +++ b/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; $i++) { diff --git a/norm_scripts/runall_normalization.pl b/norm_scripts/runall_normalization.pl index 3240fde..22a1041 100644 --- a/norm_scripts/runall_normalization.pl +++ b/norm_scripts/runall_normalization.pl @@ -612,7 +612,7 @@ } } open(LOG, ">>$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; diff --git a/template_v0.8.5.cfg b/template_v0.8.5.cfg index baeda00..65b2e42 100644 --- a/template_v0.8.5.cfg +++ b/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) ######################################################################################################################