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
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
#!/usr/bin/env python3
"""
Run the benchmarks necessary to reproduce the figures of Section 3
of the Supplementary Information of the manuscript \"Gfapy: a flexible
and extensible software library for handling sequence graphs in Python\"
and plots the figures using R.
"""
import argparse
import os
op = argparse.ArgumentParser(description=__doc__)
op.add_argument("fignum", help="Figure number", type=int,
choices=range(5,9))
op.add_argument("--queue", default=None,
help="Use the specified queue of a Grid Engine cluster system "+
"(e.g. 16c.q). If not provided, the benchmarks are run on the "+
"local computer.")
op.add_argument("--nrepl",type=int, default=3,
help="Number of replicates (default: 3)")
op.add_argument("--fast",action="store_true",
help="Run only the three fastest datapoints of the benchmark")
opts = op.parse_args()
if opts.fignum == 5:
testvar="segments"
operation="convert"
elif opts.fignum == 6:
testvar="connectivity"
operation="convert"
elif opts.fignum == 7:
testvar="segments"
operation="mergelinear"
else: # 8
testvar="connectivity"
operation="mergelinear"
if opts.fast:
subset="fast"
else:
subset="all"
run_benchmarks_args="figure{}.out {} gfa2 {} {} {}".format(
opts.fignum, operation, testvar, subset, opts.nrepl)
if not opts.queue:
os.system("./gfapy-run-benchmarks.sh {}".format(run_benchmarks_args))
else:
qsub_script_pfx=\
"""#!/bin/bash
#$ -clear
#$ -q {}
#$ -cwd
#$ -V
#$ -S /bin/bash
#$ -o jobs_out
#$ -j y
#$ -sync y
""".format(opts.queue)
with open("gfapy-run-benchmarks.sh", "r") as input_file:
content = input_file.read()
with open("gfapy-run-benchmarks.qsub", "w") as output_file:
output_file.write(qsub_script_pfx)
output_file.write(content)
os.system("mkdir -p jobs_out")
os.system("qsub gfapy-run-benchmarks.qsub {}".format(run_benchmarks_args))
if testvar == "segments":
prepareflag=""
else:
prepareflag="--mult"
os.system("./gfapy-plot-preparedata.py {} figure{}.out > figure{}.dat".format(
prepareflag, opts.fignum, opts.fignum))
os.system("./gfapy-plot-benchmarkdata.R figure{}.dat figure{} {}".format(
opts.fignum, opts.fignum, testvar))
|
