From 1015b463e22468698474744317e6e252bb58e2cc Mon Sep 17 00:00:00 2001
From: Ramya Raviram <ramya617@gmail.com>
Date: Thu, 15 Aug 2019 23:36:57 -0700
Subject: [PATCH] Update reduced_genome.sh

line 31 - comment: added unique
---
 reduced_genome.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reduced_genome.sh b/reduced_genome.sh
index f5f0930..48a4a36 100644
--- a/reduced_genome.sh
+++ b/reduced_genome.sh
@@ -28,7 +28,7 @@ cat up.txt down.txt > ${genome}_${enzyme}_flanking_sites_${fl}_2.bed
 awk '{if($2 >= 0 && $3 >=0) print $0}' ${genome}_${enzyme}_flanking_sites_${fl}_2.bed | grep -v -E 'random|JH|GL' - | sort -k1,1 -k2,2n | uniq  > ${genome}_${enzyme}_flanking_sites_${fl}_unique_2.bed
 #get the sequence of unique flanking coordinates
 fastaFromBed -fi ${genome}.fa -bed ${genome}_${enzyme}_flanking_sites_${fl}_unique_2.bed -fo ${genome}_${enzyme}_flanking_sequences_${fl}_unique_2.fa
-#get only sequences from FASTA file
+#get only unique sequences from FASTA file
 grep -v '^>' ${genome}_${enzyme}_flanking_sequences_${fl}_unique_2.fa | sort | uniq -i -u | grep -xF -f - -B 1 ${genome}_${enzyme}_flanking_sequences_${fl}_unique_2.fa | grep -v '^--' > ${genome}_${enzyme}_flanking_sequences_${fl}_unique.fa
 
 #remove unwanted intermediate files