BOL: Loop over with all files in a directory in bash

BioScripts
Jit
Loop over with all files in a directory in bash

Loop over with all files in a directory in bash

By Jit 2535 days ago

#!/bin/bash
FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/*
ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna
path=/home/urbe/Tools/SATSUMA/satsuma-code-0
for f in $FILES
do
  if [ ${f: -4} == ".fna" ]; then
  echo "Processing $f file..."
  ff=$(basename "${f%.*}")
echo $ff
  # take action on each file. $f store current file name
  mkdir $ff
  $path/SatsumaSynteny -q $ref -t $f -o $ff
  #cat $f
  fi
done

BOL

Jit

Our Sponsors

Loop over with all files in a directory in bash