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
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
|
#!/usr/bin/python3
# 1. predict
# 2. cluster
# 3. rename
# 4. snps
import biotools.analysis.run as pr
import biotools.analysis.cluster as cw
import biotools.analysis.renamer as mv
import biotools.analysis.variance as cs
import biotools.analysis.options as op
import biotools.analysis.loaddata as ld
import sys
import os
if __name__ == "__main__":
op.parse(sys.argv[1:])
if len(op.args) < 2:
op.help()
exit(0)
direc = op.DIRECTORY
plotter = op.PLOTTER
database = op.args[0]
names = op.args[1:]
sep = os.sep
predict = op.predicting
cluster = op.clustering
rename = op.renaming
plot = op.plotting
report = op.reporting
calculate = op.calculating
rename = rename and (cluster or not predict)
calculate = calculate and (cluster or not predict)
plot = plot and (calculate or not (predict or cluster))
report = report and calculate
if not (predict or cluster or rename or calculate or plot or report):
print("I don't know what you want, I give up.")
exit(0)
if predict:
names = pr.run(database, names)
print("Homologous sequences written to " + direc + 'sequences' + sep)
if cluster:
names = cw.run(direc + 'clusters' + sep, names)
print("Clustalw files written to " + direc + "clusters" + sep)
if rename:
names = mv.rename(direc + 'clusters' + sep, database, names)
if plot and plotter.lower() != 'none':
try:
cv = __import__(plotter, globals(), locals(), ['plot'], -1)
except ImportError:
try:
if not plotter.endswith('.py'):
plotter += '.py'
open(plotter, 'r')
except:
plot = False
else:
p = plotter.rfind(sep)
if p > -1:
sys.path.append(plotter[:p])
plotter = plotter[p + len(sep):]
try:
cv = __import__(plotter, globals(), locals(), ['plot'], -1)
except ImportError:
plot = False
if calculate:
gen = cs.var(names)
elif plot:
gen = (ld.parse(s) for s in names)
else:
gen = []
for entry in gen:
plotdata = entry['plotdata']
metadata = entry['metadata']
if plot:
try:
cv.plot(plotdata, direc + 'plots' + sep,
filename=metadata['filename'])
except Exception as e:
print(metadata['filename'], e)
if report:
try:
os.mkdir(direc + 'data' + sep)
except:
pass
fh = open(direc + 'data' + sep + metadata['strain'] + '.py', 'w')
fh.write('plotdata = ' + repr(plotdata) + '\n')
fh.write('metadata = ' + repr(metadata) + '\n')
print("Done")
|
