output to a variable file name in for loop in bash

Question

I am doing some tasks in side the for loop and trying to stdout to a variable file name during every iteration. But it is giving me the only one file with part of file assigned.

This is my script:

#!/bin/sh
me1_dir="/Users/njayavel/Downloads/Silencer_project/roadmap_analysis/data/h3k4me1_data"
me3_dir="/Users/njayavel/Downloads/Silencer_project/roadmap_analysis/data/h3k4me3_data"
dnase_dir="/Users/njayavel/Downloads/Silencer_project/roadmap_analysis/data/dnase_data"
index=(003 004)
#index=(003 004 005 006 007 008 017 021 022 028 029 032 033 034 046 050 051 055 056 057 059 080 081 082 083 084 085 086 088 089 090 091 092 093 094 097 098 100 109)
#index=(006 007 008 017 021 022 028 029 032 033 034 046 050 051 055 056 057 059 080 081 082 083 084 085 086 088 089 090 091 092 093 094 097 098 100 109)
for i in "${index[@]}"; do     
dnase_file="$dnase_dir/E$i-DNase.hotspot.fdr0.01.broad.bed"
me1_fil="$me1_dir/E$i-H3K4me1.broadPeak"
me3_fil="$me3_dir/E$i-H3K4me3.broadPeak"
awk 'BEGIN { OFS="\t"}; {print $1,$2,$3}' $me1_fil > me1_file.bed
awk 'BEGIN { OFS="\t"}; {print $1,$2,$3}' $me3_fil > me3_file.bed
ctcf_file="CTCFsites_hg19_sorted_bedmerged.bed"
tss_file="TSS_gene_2kbupstrm_0.5kbdownstrm.bed"
cat me1_file.bed me3_file.bed $ctcf_file $tss_file | sort -k1,1 -k2,2n > file2.bed
awk 'BEGIN { OFS="\t"}; {print $1,$2,$3}' $dnase_file | sort -k1,1 -k2,2n > file1.bed
bedtools intersect -v -a file1.bed -b file2.bed > E$i_file.txt;
done

It is giving only the output file "E.txt" from the last line in for loop. I am expecting E003_file.txt and E004_file.txt.

I am newbie please help me out. Thank you

Answer 1

When you write

E$i_file.txt

the shell is looking for a variable named i_file, because _ is a valid character in a variable name, not a delimiter. You need to use braces to delimit the variable name:

bedtools intersect -v -a file1.bed -b file2.bed > "E${i}_file.txt"