Source Code for Module Bio.Wise.psw

  1  #!/usr/bin/env python 
  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  # Bio.Wise contains modules for running and processing the output of 
  7  # some of the models in the Wise2 package by Ewan Birney available from: 
  8  # ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ 
  9  # http://www.ebi.ac.uk/Wise2/ 
 10  # 
 11  # Bio.Wise.psw is for protein Smith-Waterman alignments 
 12  # Bio.Wise.dnal is for Smith-Waterman DNA alignments 
 13   
 14  __version__ = "$Revision: 1.5 $" 
 15   
 16  import os 
 17  import re 
 18  import sys 
 19   
 20  from Bio import Wise 
 21   
 22  _CMDLINE_PSW = ["psw", "-l", "-F"] 
 23  _OPTION_GAP_START = "-g" 
 24  _OPTION_GAP_EXTENSION = "-e" 
 25  _OPTION_SCORES = "-m" 
 26   
 27   
 28 -class AlignmentColumnFullException(Exception): 
 29      pass 
 30   
 31   
 32 -class Alignment(list): 
 33 -    def append(self, column_unit): 
 34          try: 
 35              self[-1].append(column_unit) 
 36          except AlignmentColumnFullException: 
 37              list.append(self, AlignmentColumn(column_unit)) 
 38          except IndexError: 
 39              list.append(self, AlignmentColumn(column_unit)) 
 40   
 41   
 42 -class AlignmentColumn(list): 
 43 -    def _set_kind(self, column_unit): 
 44          if self.kind == "SEQUENCE": 
 45              self.kind = column_unit.kind 
 46   
 47 -    def __init__(self, column_unit): 
 48          assert column_unit.unit == 0 
 49          self.kind = column_unit.kind 
 50          list.__init__(self, [column_unit.column, None]) 
 51   
 52 -    def __repr__(self): 
 53          return "%s(%s, %s)" % (self.kind, self[0], self[1]) 
 54   
 55 -    def append(self, column_unit): 
 56          if self[1] is not None: 
 57              raise AlignmentColumnFullException 
 58   
 59          assert column_unit.unit == 1 
 60   
 61          self._set_kind(column_unit) 
 62          self[1] = column_unit.column 
 63   
 64   
 65 -class ColumnUnit(object): 
 66 -    def __init__(self, unit, column, kind): 
 67          self.unit = unit 
 68          self.column = column 
 69          self.kind = kind 
 70   
 71 -    def __str__(self): 
 72          return "ColumnUnit(unit=%s, column=%s, %s)" % (self.unit, self.column, self.kind) 
 73   
 74      __repr__ = __str__ 
 75   
 76  _re_unit = re.compile(r"^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$") 
 77   
 78   
 79 -def parse_line(line): 
 80      """ 
 81      >>> print parse_line("Column 0:") 
 82      None 
 83      >>> parse_line("Unit  0- [  -1-   0] [SEQUENCE]") 
 84      ColumnUnit(unit=0, column=0, SEQUENCE) 
 85      >>> parse_line("Unit  1- [  85-  86] [SEQUENCE]") 
 86      ColumnUnit(unit=1, column=86, SEQUENCE) 
 87      """ 
 88      match = _re_unit.match(line.rstrip()) 
 89   
 90      if not match: 
 91          return 
 92   
 93      return ColumnUnit(int(match.group(1)), int(match.group(3)), match.group(4)) 
 94   
 95   
 96 -def parse(iterable): 
 97      """ 
 98      format 
 99   
100      Column 0: 
101      Unit  0- [  -1-   0] [SEQUENCE] 
102      Unit  1- [  85-  86] [SEQUENCE] 
103   
104      means that seq1[0] == seq2[86] (0-based) 
105      """ 
106   
107      alignment = Alignment() 
108      for line in iterable: 
109          try: 
110              if os.environ["WISE_PY_DEBUG"]: 
111                  print line, 
112          except KeyError: 
113              pass 
114   
115          column_unit = parse_line(line) 
116          if column_unit: 
117              alignment.append(column_unit) 
118   
119      return alignment 
120   
121   
122 -def align(pair, 
123            scores=None, 
124            gap_start=None, 
125            gap_extension=None, 
126            *args, **keywds): 
127   
128      cmdline = _CMDLINE_PSW[:] 
129      if scores: 
130          cmdline.extend((_OPTION_SCORES, scores)) 
131      if gap_start: 
132          cmdline.extend((_OPTION_GAP_START, str(gap_start))) 
133      if gap_extension: 
134          cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension))) 
135      temp_file = Wise.align(cmdline, pair, *args, **keywds) 
136      return parse(temp_file) 
137   
138   
139 -def main(): 
140      print align(sys.argv[1:3]) 
141   
142   
143 -def _test(*args, **keywds): 
144      import doctest 
145      doctest.testmod(sys.modules[__name__], *args, **keywds) 
146   
147  if __name__ == "__main__": 
148      if __debug__: 
149          _test() 
150      main() 
151