Source Code for Package Bio.Wise

  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: 1.17 $" 
 15   
 16  import os 
 17  import sys 
 18  import tempfile 
 19   
 20  from Bio import SeqIO 
 21   
 22   
 23 -def _build_align_cmdline(cmdline, pair, output_filename, kbyte=None, force_type=None, quiet=False): 
 24      """Helper function to build a command line string (PRIVATE). 
 25   
 26      >>> os.environ["WISE_KBYTE"]="300000" 
 27      >>> if os.isatty(sys.stderr.fileno()): 
 28      ...    c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), 
 29      ...                             "/tmp/output", kbyte=100000) 
 30      ...    assert c == 'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output', c 
 31      ...    c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), 
 32      ...                             "/tmp/output_aa") 
 33      ...    assert c == 'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa', c 
 34      ... else: 
 35      ...    c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), 
 36      ...                             "/tmp/output", kbyte=100000) 
 37      ...    assert c == 'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output', c 
 38      ...    c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), 
 39      ...                             "/tmp/output_aa") 
 40      ...    assert c == 'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa', c 
 41   
 42      """ 
 43      cmdline = cmdline[:] 
 44   
 45      ### XXX: force_type ignored 
 46   
 47      if kbyte is None: 
 48          try: 
 49              cmdline.extend(("-kbyte", os.environ["WISE_KBYTE"])) 
 50          except KeyError: 
 51              pass 
 52      else: 
 53          cmdline.extend(("-kbyte", str(kbyte))) 
 54   
 55      if not os.isatty(sys.stderr.fileno()): 
 56          cmdline.append("-quiet") 
 57   
 58      cmdline.extend(pair) 
 59      cmdline.extend((">", output_filename)) 
 60      if quiet: 
 61          cmdline.extend(("2>", "/dev/null")) 
 62      cmdline_str = ' '.join(cmdline) 
 63   
 64      return cmdline_str 
 65   
 66   
 67 -def align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False): 
 68      """ 
 69      Returns a filehandle 
 70      """ 
 71      assert len(pair) == 2 
 72   
 73      output_file = tempfile.NamedTemporaryFile(mode='r') 
 74      input_files = tempfile.NamedTemporaryFile(mode="w"), tempfile.NamedTemporaryFile(mode="w") 
 75   
 76      if dry_run: 
 77          print _build_align_cmdline(cmdline, 
 78                                     pair, 
 79                                     output_file.name, 
 80                                     kbyte, 
 81                                     force_type, 
 82                                     quiet) 
 83          return 
 84   
 85      for filename, input_file in zip(pair, input_files): 
 86          # Pipe the file through Biopython's Fasta parser/writer 
 87          # to make sure it conforms to the Fasta standard (in particular, 
 88          # Wise2 may choke on long lines in the Fasta file) 
 89          records = SeqIO.parse(open(filename), 'fasta') 
 90          SeqIO.write(records, input_file, 'fasta') 
 91          input_file.flush() 
 92   
 93      input_file_names = [input_file.name for input_file in input_files] 
 94   
 95      cmdline_str = _build_align_cmdline(cmdline, 
 96                                         input_file_names, 
 97                                         output_file.name, 
 98                                         kbyte, 
 99                                         force_type, 
100                                         quiet) 
101   
102      if debug: 
103          print >>sys.stderr, cmdline_str 
104   
105      status = os.system(cmdline_str) >> 8 
106   
107      if status > 1: 
108          if kbyte != 0: # possible memory problem; could be None 
109              print >>sys.stderr, "INFO trying again with the linear model" 
110              return align(cmdline, pair, 0, force_type, dry_run, quiet, debug) 
111          else: 
112              raise OSError("%s returned %s" % (" ".join(cmdline), status)) 
113   
114      return output_file 
115   
116   
117 -def all_pairs(singles): 
118      """ 
119      Generate pairs list for all-against-all alignments 
120   
121      >>> all_pairs(range(4)) 
122      [(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)] 
123      """ 
124      pairs = [] 
125   
126      singles = list(singles) 
127      while singles: 
128          suitor = singles.pop(0) # if sorted, stay sorted 
129          pairs.extend([(suitor, single) for single in singles]) 
130   
131      return pairs 
132   
133   
134 -def main(): 
135      pass 
136   
137   
138 -def _test(*args, **keywds): 
139      import doctest 
140      doctest.testmod(sys.modules[__name__], *args, **keywds) 
141   
142  if __name__ == "__main__": 
143      if __debug__: 
144          _test() 
145      main() 
146