Provean Sus scrofa

From Variant Effect Predictor output, select only protein altering variants and sort by transcript:

cat outVEP_*.txt | awk '$11~/\//' | sed 's/:/\t/' | sort -k6 >prot_alt.txt

Protein models for Sus scrofa:

 /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa

!/bin/bash
#SBATCH --time=4800
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=16000
#SBATCH --nice=1000
#SBATCH --output=output_%j.txt
#SBATCH --error=error_output_%j.txt
#SBATCH --job-name=Provean
#SBATCH --partition=ABGC_Research
#cat outVEP_*.txt | awk '$11~/\//' | sed 's/:/\t/' | sort -k6 >prot_alt.txt
TELLER=100
echo $TELLER;
let TELLER+=1;
echo $TELLER;
while [ $TELLER -gt 99 ]; do

  PROVS=`squeue | grep Provean | sed 's/^ \+//' | sed 's/ \+/\t/' | cut -f1`;
  for PROV in $PROVS; do scancel $PROV; done;
  sleep 10;
  for i in `seq 1 2`; do ssh fat00$i 'rm -rf /tmp/provean*'; done;
  for i in `seq 10 60`; do ssh node0$i 'rm -rf /tmp/provean*'; done;
  for i in `seq 1 9`; do ssh node00$i 'rm -rf /tmp/provean*'; done;
  TRANS=`cat prot_alt.txt | head -15000 | cut -f6 | sort | uniq`;
  TELLER2=0;
  for TRAN in $TRANS; do
     if [ $TELLER2 -lt 300 ]; then
       echo "transcript: $TRAN";
       echo "teller boven: $TELLER2";
       PROT=`cat /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Sscrofa10.2.74.pep.all.fa | grep $TRAN | sed 's/ \+/\t/g' | sed 's/^>//' | cut -f1`;
       echo "protein: $PROT";
       if [ -f $PROT.sss ];
        then
          echo "$PROT $TRAN already done";
        else
          echo "will do sbatch testProvean_sub.sh $TRAN'";
          sbatch testProvean_sub.sh $TRAN;
          let TELLER2+=1;
          echo "teller onder: $TELLER2";
       fi;
    fi;
  done;
  sleep 3600;
done