fasta_check.sh

#!/bin/bash -l
#SBATCH -D /home/dmvelasc/Projects/Prunus/Analysis/selection
#SBATCH -o /home/dmvelasc/Projects/Prunus/slurm-log/%j-facheck-stdout.txt
#SBATCH -e /home/dmvelasc/Projects/Prunus/slurm-log/%j-facheck-stderr.txt
#SBATCH -J facheck
#SBATCH -t 8-00:00:00
#SBATCH -n 1
#SBATCH -c 1
#SBATCH -p bigmemm
#SBATCH --mail-user=dmvelasco@ucdavis.edu
#SBATCH --mail-type=ALL
set -e
set -u

# number of genes = number of arrays = 27864
# --exclude=bigmem1,bigmem2

### Declare directories ###
ref="/home/dmvelasc/Data/references/persica-SCF"				# reference directory
gene_list="${ref}/Prunus_persica_v1.0_genes_list.gff3"				# gene list
FASTAdir="/group/jrigrp3/Velasco/Prunus/fasta/fasta-nostop"			# final fasta directory

for i in {0..27863}; do
  #### sample ID file
  mapfile -s "$i" -n 1 -t gene < "${gene_list}"
  # declare gene ID variable from array
  gene_id="${gene[0]}"

  ##### B U S T E D #####
  if [ ! -f "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" ]; then
  # if file exists and is not empty
    echo "${i}: ${gene_id}_cds_aln_nostop.fasta does not exist"
#    if [ -s "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" ]; then
#      echo "and is not an empty file."
#    else
#      echo "but is an empty file."
#    fi
  fi
done