Hi all,
please help me construct the command. i want to loop through all files named bam* and bed*. My awk works for a particular pair but there are too many pairs to do manually.
I have generated multiple files in a folder in a given pattern. The files are named like
bam_fixed1.bam
bed_fixed1.bed
bam_fixed2.bam
bed_fixed2.bed
....
.....
so that every bam file is paired with a bed file. The fixed portion of the filename is the same for a particular pair of bam and bed.
I want to construct an awk command which acts on a bam and its particular bed pair..
what I want to do is for all pairs
awk 'NR == FNR { commands }' bam_fixed1.bam bed_fixed1.bed > out_fixed1.txt
awk 'NR == FNR { commands }' bam_fixed2.bam bed_fixed2.bed > out_fixed2.txt
...
If there was only 1 file I can use a for loop like
for f in bam_*.bam
do
commands with $f
done
How do I do this for multiple files and corresponding pairs?