forked from akahanaton/multiz
-
Notifications
You must be signed in to change notification settings - Fork 0
/
count.jobs.sh
executable file
·50 lines (50 loc) · 2.19 KB
/
count.jobs.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
for queryDir in `ls -d batsGenome/[[:lower:]]*[[:upper:]]*`
#--------------------------------------------------
# for queryDir in `ls -d batsGenome/eonSpe`
#--------------------------------------------------
do
queryID="`basename $queryDir`2"
nibQueryDir="$queryDir/$queryID.nib2"
for targetDir in `ls -d ucsc/hg38`
do
targetID=`basename $targetDir`
snakeDir=snake.$queryID.$targetID
lavQueryDir="$queryDir/$queryID.$targetID.lav"
pslQueryDir="$queryDir/$queryID.$targetID.psl"
chainQueryDir="$queryDir/$queryID.$targetID.chain"
echo $snakeDir
for snake in $snakeDir/*.snake
do
queryChr=`basename $snake .snake`
#--------------------------------------------------
# mkdir $lavQueryDir/$queryChr
# mkdir $pslQueryDir/$queryChr
# mkdir $chainQueryDir/$queryChr
#--------------------------------------------------
done
#--------------------------------------------------
# mkdir $chainQueryDir/done
#--------------------------------------------------
#--------------------------------------------------
# for chain in `ls -f $chainQueryDir/done/*.chain`
# do
# queryChr=`basename $chain .chain`
# mv $chain $chainQueryDir/done
# #--------------------------------------------------
# # mv snake.$queryID.$targetID/$queryChr.* snake.$queryID.$targetID.cmd
# #--------------------------------------------------
# done
#--------------------------------------------------
if [ "$(ls -A $chainQueryDir/merge)" ]; then
mv $chainQueryDir/merge/*.chain $chainQueryDir/done/
fi
find $nibQueryDir/ -name "*.nib" | wc -l
find $chainQueryDir/done/ -name "*.chain" | wc -l
find $chainQueryDir/merge/ -name "*.chain" | wc -l
find $snakeDir/ -name "*.snake" | wc -l
find $snakeDir/ -name "*.cmd" | wc -l
#--------------------------------------------------
# find snake.$queryID.$targetID.cmd/ -name "*.snake" | wc -l
#--------------------------------------------------
done
done