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
|
#!/bin/bash -e
rm -f single* search_* blits_*
if $(command -v "ffindex_apply_mpi" >/dev/null 2>&1); then
MPI=1
fi
hhalign -i query.a3m -t query.a3m
ffindex_build -s single.ffdata single.ffindex query.a3m
APPLY="ffindex_apply"
if [ -n "$MPI" ]; then
APPLY="mpirun -np 2 ffindex_apply_mpi"
fi
$APPLY single.ffdata single.ffindex -d single_a3m_cons.ffdata -i single_a3m_cons.ffindex \
-- hhconsensus -i stdin -oa3m stdout -M a3m -v 0
$APPLY single_a3m_cons.ffdata single_a3m_cons.ffindex -d single_a3m.ffdata -i single_a3m.ffindex \
-- hhfilter -i stdin -o stdout -diff 1000 -v 0
$APPLY single_a3m.ffdata single_a3m.ffindex -d single_hhm.ffdata -i single_hhm.ffindex \
-- hhmake -i stdin -o stdout -v 0
if [ -n "$MPI" ]; then
mpirun -np 2 cstranslate_mpi -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m
else
cstranslate -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m -f
fi
hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
hhblits_omp -i single -d single -blasttab blits_omp_res -n 1
diff <(tr -d '\000' < blits_omp_res.ffdata) blits_app_res
if [ -n "$MPI" ]; then
mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
fi
hhsearch -i query.a3m -d single -blasttab search_app_res
hhsearch_omp -i single -d single -blasttab search_omp_res
diff <(tr -d '\000' < search_omp_res.ffdata) search_app_res
if [ -n "$MPI" ]; then
mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
diff <(tr -d '\000' < search_mpi_res.ffdata) search_app_res
fi
diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)
|
