Provean Sus scrofa
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From Variant Effect Predictor output, select only protein altering variants and sort by transcript: <source lang='bash'> cat outVEP_*.txt | awk '$11~/\//' | sed 's/:/\t/' | sort -k6 >prot_alt.txt </source>
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
<source lang='bash'>
!/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
</source>