Source Code for Module Bio.Phylo.PAML.yn00

  1  # Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com) 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license. Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6  import os.path 
  7  from _paml import Paml 
  8  import _parse_yn00 
  9   
 10  #TODO - Restore use of with statement for closing handles automatically 
 11  #after dropping Python 2.4 
 12   
 13   
 14 -class Yn00Error(EnvironmentError): 
 15      """yn00 has failed. Run with verbose = True to view yn00's error 
 16  message""" 
 17   
 18   
 19 -class Yn00(Paml): 
 20      """This class implements an interface to yn00, part of the PAML package.""" 
 21   
 22 -    def __init__(self, alignment = None, working_dir = None, 
 23                  out_file = None): 
 24          """Initialize the Yn00 instance. 
 25   
 26          The user may optionally pass in strings specifying the locations 
 27          of the input alignment, the working directory and 
 28          the final output file. 
 29          """ 
 30          Paml.__init__(self, alignment, working_dir, out_file) 
 31          self.ctl_file = "yn00.ctl" 
 32          self._options = {"verbose": None, 
 33                          "icode": None, 
 34                          "weighting": None, 
 35                          "commonf3x4": None, 
 36                          "ndata": None} 
 37   
 38 -    def write_ctl_file(self): 
 39          """Dynamically build a yn00 control file from the options. 
 40   
 41          The control file is written to the location specified by the 
 42          ctl_file property of the yn00 class. 
 43          """ 
 44          # Make sure all paths are relative to the working directory 
 45          self._set_rel_paths() 
 46          if True:  # Dummy statement to preserve indentation for diff 
 47              ctl_handle = open(self.ctl_file, 'w') 
 48              ctl_handle.write("seqfile = %s\n" % self._rel_alignment) 
 49              ctl_handle.write("outfile = %s\n" % self._rel_out_file) 
 50              for option in self._options.items(): 
 51                  if option[1] is None: 
 52                      # If an option has a value of None, there's no need 
 53                      # to write it in the control file; it's normally just 
 54                      # commented out. 
 55                      continue 
 56                  ctl_handle.write("%s = %s\n" % (option[0], option[1])) 
 57              ctl_handle.close() 
 58   
 59 -    def read_ctl_file(self, ctl_file): 
 60          """Parse a control file and load the options into the yn00 instance. 
 61          """ 
 62          temp_options = {} 
 63          if not os.path.isfile(ctl_file): 
 64              raise IOError("File not found: %r" % ctl_file) 
 65          else: 
 66              ctl_handle = open(ctl_file) 
 67              for line in ctl_handle: 
 68                  line = line.strip() 
 69                  uncommented = line.split("*",1)[0] 
 70                  if uncommented != "": 
 71                      if "=" not in uncommented: 
 72                          ctl_handle.close() 
 73                          raise AttributeError( 
 74                              "Malformed line in control file:\n%r" % line) 
 75                      (option, value) = uncommented.split("=") 
 76                      option = option.strip() 
 77                      value = value.strip() 
 78                      if option == "seqfile": 
 79                          self.alignment = value 
 80                      elif option == "outfile": 
 81                          self.out_file = value 
 82                      elif option not in self._options: 
 83                          ctl_handle.close() 
 84                          raise KeyError("Invalid option: %s" % option) 
 85                      else: 
 86                          if "." in value or "e-" in value: 
 87                              try: 
 88                                  converted_value = float(value) 
 89                              except: 
 90                                  converted_value = value 
 91                          else: 
 92                              try: 
 93                                  converted_value = int(value) 
 94                              except: 
 95                                  converted_value = value 
 96                          temp_options[option] = converted_value 
 97              ctl_handle.close() 
 98          for option in self._options.keys(): 
 99              if option in temp_options.keys(): 
100                  self._options[option] = temp_options[option] 
101              else: 
102                  self._options[option] = None 
103   
104 -    def run(self, ctl_file = None, verbose = False, command = "yn00", 
105                  parse = True): 
106          Paml.run(self, ctl_file, verbose, command) 
107          if parse: 
108              results = read(self.out_file) 
109          else: 
110              results = None 
111          return results 
112   
113   
114 -def read(results_file): 
115      """Parse a yn00 results file.""" 
116      results = {} 
117      if not os.path.exists(results_file): 
118          raise IOError("Results file does not exist.") 
119      handle = open(results_file) 
120      lines = handle.readlines() 
121      handle.close() 
122      for line_num in range(len(lines)): 
123          line = lines[line_num] 
124          if "(A) Nei-Gojobori (1986) method" in line: 
125              ng86_start = line_num + 1 
126          elif "(B) Yang & Nielsen (2000) method" in line: 
127              (results, sequences) = _parse_yn00.parse_ng86(lines[ng86_start:line_num], 
128                      results) 
129              yn00_start = line_num + 1 
130          elif "(C) LWL85, LPB93 & LWLm methods" in line: 
131              results = _parse_yn00.parse_yn00(lines[yn00_start:line_num], results, 
132                      sequences) 
133              results = _parse_yn00.parse_others(lines[line_num+1:], results, 
134                      sequences) 
135      if len(results) == 0: 
136          raise ValueError("Invalid results file.") 
137      return results 
138