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clean_finished_snake.sh
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clean_finished_snake.sh
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#!/usr/bin/env bash
set –euo pipefail
#--------------------------------------------------
# dir=snake.pteAle2.eonSpe2
# for snake in `ls -f ./$dir/*.snake`
# do
# if [[ -e $snake.cmd ]]; then
# mv ${snake} ./$dir.cmd
# fi
# done
#--------------------------------------------------
queryID=pteAle
targetID=eonSpe
queryID2=${queryID}2
targetID2=${targetID}2
for cmd in `ls -f snake.$queryID2.$targetID2/ | grep 'cmd$'`
do
queryChr=`basename $cmd .snake.cmd`
if [[ -e ./batsGenome/$queryID/$queryID2.$targetID2.chain/$queryChr.chain.list ]]; then
mv snake.$queryID2.$targetID2/$cmd snake.$queryID2.$targetID2.cmd
echo $queryChr
#--------------------------------------------------
# find batsGenome/$queryID/$queryID2.$targetID2.chain/$queryChr -delete
# find batsGenome/$queryID/$queryID2.$targetID2.lav/$queryChr -delete
# find batsGenome/$queryID/$queryID2.$targetID2.psl/$queryChr -delete
#--------------------------------------------------
fi
done