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
51
52
53
54
|
foo(){
#cut -f 2 mstime > mstmrca
#cut -f 2 scrmtime > scrmtmrca
echo "TMRCA" > figuretitle
R CMD BATCH tmrca.r
#cut -f 3 mstime > msbl
#cut -f 3 scrmtime > scrmbl
echo "BL" > figuretitle
R CMD BATCH bl.r
cut -f 6 ms_stats > msdata
cut -f 6 scrm_stats > scrmdata
echo "Tajima_D" > figuretitle
R CMD BATCH ks.r
cut -f 2 ms_stats > msdata
cut -f 2 scrm_stats > scrmdata
echo "Pairewise_difference" > figuretitle
R CMD BATCH ks.r
cut -f 8 ms_stats > msdata
cut -f 8 scrm_stats > scrmdata
echo "theta_H" > figuretitle
R CMD BATCH ks.r
cut -f 10 ms_stats > msdata
cut -f 10 scrm_stats > scrmdata
echo "H" > figuretitle
R CMD BATCH ks.r
}
mstime(){
cat msout | gawk '/^\/\//{f="xx"++d} f{print > f} '
for file in $(seq 1 1 ${rep})
do
grep ";" xx${file} | sed -e 's/\[.*\]//g' | tail -1 >> msTrees
done
hybrid-Lambda -gt msTrees -tmrca mstmrca
hybrid-Lambda -gt msTrees -bl msbl
find . -name "xx*" -print0 | xargs -0 rm
}
scrmtime(){
cat scrmout | gawk '/^\/\//{f="xx"++d} f{print > f} '
for file in $(seq 1 1 ${rep})
do
grep ";" xx${file} | sed -e 's/\[.*\]//g' | tail -1 >> scrmTrees
done
hybrid-Lambda -gt scrmTrees -tmrca scrmtmrca
hybrid-Lambda -gt scrmTrees -bl scrmbl
find . -name "xx*" -print0 | xargs -0 rm
}
|
