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p4ann_RxLR.sh
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p4ann_RxLR.sh
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#!/bin/bash
#$ -cwd
# #$ -m bes
# #$ -M $email
#$ -S /bin/bash
#$ -N part4
#$ -o part4_outv3
#$ -e part4_errv3
#$ -l mem_free=3G
#$ -V
############ DO NOT EDIT BELOW THIS LINE ###################################################
#============================================================================================#
mkdir part4
touch part4/avh2blast2.list
ls -1 part3/avh2blast2*.list >> part4/avh2blast2.list
ablast2=( `cat "part4/avh2blast2.list" `)
#touch part4/avh2blast2rem.list
# ls -1 part3/avh2removedblast2*.list >> part4/avh2removedblast2.list
#ablastrem=( `cat "part4/avh2removedblast2.list" `)
#### Echo files that are used in this script
for t in "${ablast2[@]}"
do
echo $t
done
#for t in "${ablastrem[@]}"
# do
# echo $t
# done
####### Summarizing the number of candidate Avh candidates are identified in each blast search ###########
touch part4/summary.out
sum=part4/summary.out
#ls -1 *list >> $sum
# summarizing for blast to ramorum reference results:
# echo avh2blast2ref.list >> $sum
# sort part3/avh2blast2ref.list | wc -l >> $sum
# sort -u part3/avh2blast2ref.list | wc -l >> $sum
# echo avh2removedblast2ref.list >> $sum
# sort part3/avh2removedblast2ref.list | wc -l >> $sum
# sort -u part3/avh2removedblast2ref.list | wc -l >> $sum
# # summarizing for blast to avh family results:
# echo avh2blast2fam.list >> $sum
# sort part3/avh2blast2fam.list | wc -l >> $sum
# sort -u part3/avh2blast2fam.list | wc -l >> $sum
# echo avh2removedblast2fam.list >> $sum
# sort part3/avh2removedblast2fam.list | wc -l >> $sum
# sort -u part3/avh2removedblast2fam.list | wc -l >> $sum
for t in "${ablast2[@]}"
do
echo $t >> $sum
sort $t | wc -l >> $sum
sort -u $t | wc -l >> $sum
done
#for t in "${ablastrem[@]}"
# do
# echo $t >> $sum
# sort $t | wc -l >> $sum
# sort -u $t | wc -l >> $sum
# done
#EOF