1
2
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5
6 import os
7 import os.path
8 from _paml import Paml, PamlError, _relpath
9 import _parse_codeml
10
11
12
13
15 """CODEML has failed. Run with verbose = True to view CODEML's error
16 message"""
17
19 """This class implements an interface to CODEML, part of the PAML package."""
20
21 - def __init__(self, alignment = None, tree = None, working_dir = None,
22 out_file = None):
23 """Initialize the codeml 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. Other options found in the CODEML control
28 have typical settings by default to run site class models 0, 1 and
29 2 on a nucleotide alignment.
30 """
31 Paml.__init__(self, alignment, working_dir, out_file)
32 if tree is not None:
33 if not os.path.exists(tree):
34 raise IOError, "The specified tree file does not exist."
35 self.tree = tree
36 self.ctl_file = "codeml.ctl"
37 self._options = {"noisy": None,
38 "verbose": None,
39 "runmode": None,
40 "seqtype": None,
41 "CodonFreq": None,
42 "ndata": None,
43 "clock": None,
44 "aaDist": None,
45 "aaRatefile": None,
46 "model": None,
47 "NSsites": None,
48 "icode": None,
49 "Mgene": None,
50 "fix_kappa": None,
51 "kappa": None,
52 "fix_omega": None,
53 "omega": None,
54 "fix_alpha": None,
55 "alpha": None,
56 "Malpha": None,
57 "ncatG": None,
58 "getSE": None,
59 "RateAncestor": None,
60 "Small_Diff": None,
61 "cleandata": None,
62 "fix_blength": None,
63 "method": None}
64
66 """Dynamically build a CODEML control file from the options.
67
68 The control file is written to the location specified by the
69 ctl_file property of the codeml class.
70 """
71
72 self._set_rel_paths()
73 if True:
74 ctl_handle = open(self.ctl_file, 'w')
75 ctl_handle.write("seqfile = %s\n" % self._rel_alignment)
76 ctl_handle.write("outfile = %s\n" % self._rel_out_file)
77 ctl_handle.write("treefile = %s\n" % self._rel_tree)
78 for option in self._options.items():
79 if option[1] == None:
80
81
82
83 continue
84 if option[0] == "NSsites":
85
86
87
88 NSsites = " ".join([str(site) for site in option[1]])
89 ctl_handle.write("%s = %s\n" % (option[0], NSsites))
90 else:
91 ctl_handle.write("%s = %s\n" % (option[0], option[1]))
92 ctl_handle.close()
93
95 """Parse a control file and load the options into the Codeml instance.
96 """
97 temp_options = {}
98 if not os.path.isfile(ctl_file):
99 raise IOError("File not found: %r" % ctl_file)
100 else:
101 ctl_handle = open(ctl_file)
102 for line in ctl_handle:
103 line = line.strip()
104 uncommented = line.split("*",1)[0]
105 if uncommented != "":
106 if "=" not in uncommented:
107 ctl_handle.close()
108 raise AttributeError, \
109 "Malformed line in control file:\n%r" % line
110 (option, value) = uncommented.split("=")
111 option = option.strip()
112 value = value.strip()
113 if option == "seqfile":
114 self.alignment = value
115 elif option == "treefile":
116 self.tree = value
117 elif option == "outfile":
118 self.out_file = value
119 elif option == "NSsites":
120 site_classes = value.split(" ")
121 for n in range(len(site_classes)):
122 try:
123 site_classes[n] = int(site_classes[n])
124 except:
125 ctl_handle.close()
126 raise TypeError, \
127 "Invalid site class: %s" % site_classes[n]
128 temp_options["NSsites"] = site_classes
129 elif option not in self._options:
130 ctl_handle.close()
131 raise KeyError, "Invalid option: %s" % option
132 else:
133 if "." in value:
134 try:
135 converted_value = float(value)
136 except:
137 converted_value = value
138 else:
139 try:
140 converted_value = int(value)
141 except:
142 converted_value = value
143 temp_options[option] = converted_value
144 ctl_handle.close()
145 for option in self._options.keys():
146 if option in temp_options.keys():
147 self._options[option] = temp_options[option]
148 else:
149 self._options[option] = None
150
152 """Print out all of the options and their current settings."""
153 for option in self._options.items():
154 if option[0] == "NSsites" and option[1] is not None:
155
156
157
158 NSsites = " ".join([str(site) for site in option[1]])
159 print "%s = %s" % (option[0], NSsites)
160 else:
161 print "%s = %s" % (option[0], option[1])
162
164 """Convert all file/directory locations to paths relative to the current working directory.
165
166 CODEML requires that all paths specified in the control file be
167 relative to the directory from which it is called rather than
168 absolute paths.
169 """
170 Paml._set_rel_paths(self)
171 if self.tree is not None:
172 self._rel_tree = _relpath(self.tree, self.working_dir)
173
174 - def run(self, ctl_file = None, verbose = False, command = "codeml",
175 parse = True):
176 """Run codeml using the current configuration and then parse the results.
177
178 Return a process signal so the user can determine if
179 the execution was successful (return code 0 is successful, -N
180 indicates a failure). The arguments may be passed as either
181 absolute or relative paths, despite the fact that CODEML
182 requires relative paths.
183 """
184 if self.tree is None:
185 raise ValueError, "Tree file not specified."
186 if not os.path.exists(self.tree):
187 raise IOError, "The specified tree file does not exist."
188 Paml.run(self, ctl_file, verbose, command)
189 if parse:
190 results = read(self.out_file)
191 else:
192 results = None
193 return results
194
195 -def read(results_file):
210