1
2
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5
6 import os
7 import os.path
8 from _paml import Paml, PamlError, _relpath
9 import _parse_baseml
10
11
12
13
15 """BASEML has failed. Run with verbose = True to view BASEML's error
16 message"""
17
19 """This class implements an interface to BASEML, part of the PAML package."""
20
21 - def __init__(self, alignment = None, tree = None, working_dir = None,
22 out_file = None):
23 """Initialize the Baseml instance.
24
25 The user may optionally pass in strings specifying the locations
26 of the input alignment and tree files, the working directory and
27 the final output file.
28 """
29 Paml.__init__(self, alignment, working_dir, out_file)
30 if tree is not None:
31 if not os.path.exists(tree):
32 raise IOError, "The specified tree file does not exist."
33 self.tree = tree
34 self.ctl_file = "baseml.ctl"
35 self._options = {"noisy": None,
36 "verbose": None,
37 "runmode": None,
38 "model": None,
39 "model_options": None,
40 "Mgene": None,
41 "ndata": None,
42 "clock": None,
43 "fix_kappa": None,
44 "kappa": None,
45 "fix_alpha": None,
46 "alpha": None,
47 "Malpha": None,
48 "ncatG": None,
49 "fix_rho": None,
50 "rho": None,
51 "nparK": None,
52 "nhomo": None,
53 "getSE": None,
54 "RateAncestor": None,
55 "Small_Diff": None,
56 "cleandata": None,
57 "icode": None,
58 "fix_blength": None,
59 "method": None}
60
62 """Dynamically build a BASEML control file from the options.
63
64 The control file is written to the location specified by the
65 ctl_file property of the baseml class.
66 """
67
68 self._set_rel_paths()
69 if True:
70 ctl_handle = open(self.ctl_file, 'w')
71 ctl_handle.write("seqfile = %s\n" % self._rel_alignment)
72 ctl_handle.write("outfile = %s\n" % self._rel_out_file)
73 ctl_handle.write("treefile = %s\n" % self._rel_tree)
74 for option in self._options.items():
75 if option[1] == None:
76
77
78
79 continue
80 if option[0] == "model_options":
81 continue
82
83
84
85
86
87
88 if option[0] == "model" and option[1] in [9, 10]:
89 if self._options["model_options"] is not None:
90 ctl_handle.write("model = %s %s" % (option[1],
91 self._options["model_options"]))
92 continue
93 ctl_handle.write("%s = %s\n" % (option[0], option[1]))
94 ctl_handle.close()
95
97 """Parse a control file and load the options into the Baseml instance.
98 """
99 temp_options = {}
100 if not os.path.isfile(ctl_file):
101 raise IOError("File not found: %r" % ctl_file)
102 else:
103 ctl_handle = open(ctl_file)
104 for line in ctl_handle:
105 line = line.strip()
106 uncommented = line.split("*",1)[0]
107 if uncommented != "":
108 if "=" not in uncommented:
109 ctl_handle.close()
110 raise AttributeError, \
111 "Malformed line in control file:\n%r" % line
112 (option, value) = uncommented.split("=")
113 option = option.strip()
114 value = value.strip()
115 if option == "seqfile":
116 self.alignment = value
117 elif option == "treefile":
118 self.tree = value
119 elif option == "outfile":
120 self.out_file = value
121 elif option not in self._options:
122 ctl_handle.close()
123 raise KeyError, "Invalid option: %s" % option
124 elif option == "model":
125 if len(value) <= 2 and value.isdigit():
126 temp_options["model"] = int(value)
127 temp_options["model_options"] = None
128 else:
129 model_num = value.partition(" ")[0]
130 model_opt = value.partition(" ")[2].strip()
131 temp_options["model"] = int(model_num)
132 temp_options["model_options"] = model_opt
133 else:
134 if "." in value or "e-" in value:
135 try:
136 converted_value = float(value)
137 except:
138 converted_value = value
139 else:
140 try:
141 converted_value = int(value)
142 except:
143 converted_value = value
144 temp_options[option] = converted_value
145 ctl_handle.close()
146 for option in self._options.keys():
147 if option in temp_options.keys():
148 self._options[option] = temp_options[option]
149 else:
150 self._options[option] = None
151
153 """Convert all file/directory locations to paths relative to the current working directory.
154
155 BASEML requires that all paths specified in the control file be
156 relative to the directory from which it is called rather than
157 absolute paths.
158 """
159 Paml._set_rel_paths(self)
160 if self.tree is not None:
161 self._rel_tree = _relpath(self.tree, self.working_dir)
162
163 - def run(self, ctl_file = None, verbose = False, command = "baseml",
164 parse = True):
165 """Run baseml using the current configuration and then parse the results.
166
167 Return a process signal so the user can determine if
168 the execution was successful (return code 0 is successful, -N
169 indicates a failure). The arguments may be passed as either
170 absolute or relative paths, despite the fact that BASEML
171 requires relative paths.
172 """
173 if self.tree is None:
174 raise ValueError, "Tree file not specified."
175 if not os.path.exists(self.tree):
176 raise IOError, "The specified tree file does not exist."
177 Paml.run(self, ctl_file, verbose, command)
178 if parse:
179 results = read(self.out_file)
180 else:
181 results = None
182 return results
183
184 -def read(results_file):
197