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
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
|
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os.path
from ._paml import Paml
from . import _parse_yn00
# TODO - Restore use of with statement for closing handles automatically
# after dropping Python 2.4
class Yn00Error(EnvironmentError):
"""yn00 has failed. Run with verbose = True to view yn00's error
message"""
class Yn00(Paml):
"""This class implements an interface to yn00, part of the PAML package."""
def __init__(self, alignment=None, working_dir=None, out_file=None):
"""Initialize the Yn00 instance.
The user may optionally pass in strings specifying the locations
of the input alignment, the working directory and
the final output file.
"""
Paml.__init__(self, alignment, working_dir, out_file)
self.ctl_file = "yn00.ctl"
self._options = {"verbose": None,
"icode": None,
"weighting": None,
"commonf3x4": None,
"ndata": None}
def write_ctl_file(self):
"""Dynamically build a yn00 control file from the options.
The control file is written to the location specified by the
ctl_file property of the yn00 class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
with open(self.ctl_file, 'w') as ctl_handle:
ctl_handle.write("seqfile = %s\n" % self._rel_alignment)
ctl_handle.write("outfile = %s\n" % self._rel_out_file)
for option in self._options.items():
if option[1] is None:
# If an option has a value of None, there's no need
# to write it in the control file; it's normally just
# commented out.
continue
ctl_handle.write("%s = %s\n" % (option[0], option[1]))
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the yn00 instance.
"""
temp_options = {}
if not os.path.isfile(ctl_file):
raise IOError("File not found: %r" % ctl_file)
else:
with open(ctl_file) as ctl_handle:
for line in ctl_handle:
line = line.strip()
uncommented = line.split("*", 1)[0]
if uncommented != "":
if "=" not in uncommented:
raise AttributeError(
"Malformed line in control file:\n%r" % line)
(option, value) = uncommented.split("=")
option = option.strip()
value = value.strip()
if option == "seqfile":
self.alignment = value
elif option == "outfile":
self.out_file = value
elif option not in self._options:
raise KeyError("Invalid option: %s" % option)
else:
if "." in value or "e-" in value:
try:
converted_value = float(value)
except:
converted_value = value
else:
try:
converted_value = int(value)
except:
converted_value = value
temp_options[option] = converted_value
for option in self._options:
if option in temp_options:
self._options[option] = temp_options[option]
else:
self._options[option] = None
def run(self, ctl_file=None, verbose=False, command="yn00", parse=True):
Paml.run(self, ctl_file, verbose, command)
if parse:
results = read(self.out_file)
else:
results = None
return results
def read(results_file):
"""Parse a yn00 results file."""
results = {}
if not os.path.exists(results_file):
raise IOError("Results file does not exist.")
with open(results_file) as handle:
lines = handle.readlines()
for line_num in range(len(lines)):
line = lines[line_num]
if "(A) Nei-Gojobori (1986) method" in line:
ng86_start = line_num + 1
elif "(B) Yang & Nielsen (2000) method" in line:
(results, sequences) = _parse_yn00.parse_ng86(lines[ng86_start:line_num],
results)
yn00_start = line_num + 1
elif "(C) LWL85, LPB93 & LWLm methods" in line:
results = _parse_yn00.parse_yn00(lines[yn00_start:line_num], results,
sequences)
results = _parse_yn00.parse_others(lines[line_num + 1:], results,
sequences)
if len(results) == 0:
raise ValueError("Invalid results file.")
return results
|
