only rerun failed annotation 3 times

fei0810 · May 10, 2021 · 19587bb · 19587bb
1 parent 7c43e7e
commit 19587bb
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Showing 2 changed files with 18 additions and 6 deletions.
diff --git a/tritimap/scripts/format_blastout.sh b/tritimap/scripts/format_blastout.sh
@@ -37,10 +37,16 @@ for j in $(ls ${dir}/temp.blast.${name}split/*.fasta); do
  if [ ! -f "${j}.out.txt" ]; then
  echo $j
  python $blastpath --email $email --stype dna --program blastn --database $database --outformat out,json --outfile ${j} $j
- #TODO Control the number of cycle runs
  while [ $? -ne 0 ]; do
- echo "rerun"
- python $blastpath --email $email --stype dna --program blastn --database $database --outformat out,json --outfile ${j} $j
+ k=0
+ while ((++k)); do
+ if ((k > 3)); then
+ echo "blast ${j} failed"
+ break
+ fi
+ echo "rerun"
+ python $blastpath --email $email --stype dna --program blastn --database $database --outformat out,json --outfile ${j} $j
+ done
  done
  echo "blast ${j} done"
  shuf -i 2-5 -n1 | xargs sleep

diff --git a/tritimap/scripts/format_pfamout.sh b/tritimap/scripts/format_pfamout.sh
@@ -50,10 +50,16 @@ for j in $(ls ${dir}/temp.pfam.${name}long.pep.split/*.pep); do
  if [ ! -f "${j}.out.txt" ]; then
  echo $j
  python $scanpath --email $email --database pfam --outformat out,sequence --outfile ${j} --sequence $j
- #TODO Control the number of cycle runs
  while [ $? -ne 0 ]; do
- echo "rerun"
- python $scanpath --email $email --database pfam --outformat out,sequence --outfile ${j} --sequence $j
+ k=0
+ while ((++k)); do
+ if ((k > 3)); then
+ echo "pfam ${j} failed"
+ break
+ fi
+ echo "rerun"
+ python $scanpath --email $email --database pfam --outformat out,sequence --outfile ${j} --sequence $j
+ done
  done
  echo "pfam ${j} done"
  shuf -i 2-5 -n1 | xargs sleep