Source Code for Module Bio.Blast.ParseBlastTable

  1  # Copyright 2003 Iddo Friedberg. All rights reserved. 
  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  """A parser for the NCBI blastpgp version 2.2.5 output format. Currently only supports 
  7  the '-m 9' option, (table w/ annotations). 
  8  Returns a BlastTableRec instance 
  9  """ 
 10   
 11   
 12 -class BlastTableEntry(object): 
 13 -    def __init__(self,in_rec): 
 14          bt_fields = in_rec.split() 
 15          self.qid = bt_fields[0].split('|') 
 16          self.sid = bt_fields[1].split('|') 
 17          self.pid = float(bt_fields[2]) 
 18          self.ali_len = int(bt_fields[3]) 
 19          self.mis = int(bt_fields[4]) 
 20          self.gaps = int(bt_fields[5]) 
 21          self.q_bounds = (int(bt_fields[6]), int(bt_fields[7])) 
 22          self.s_bounds = (int(bt_fields[8]), int(bt_fields[9])) 
 23          self.e_value = float(bt_fields[10]) 
 24          self.bit_score = float(bt_fields[11]) 
 25   
 26   
 27 -class BlastTableRec(object): 
 28 -    def __init__(self): 
 29          self.program = None 
 30          self.version = None 
 31          self.date = None 
 32          self.iteration = None 
 33          self.query = None 
 34          self.database = None 
 35          self.entries = [] 
 36   
 37 -    def add_entry(self, entry): 
 38          self.entries.append(entry) 
 39   
 40  reader_keywords = {'BLASTP': 'version', 
 41                     'Iteration': 'iteration', 
 42                     'Query': 'query', 
 43                     'Database': 'database', 
 44                     'Fields': 'fields'} 
 45   
 46   
 47 -class BlastTableReader(object): 
 48 -    def __init__(self, handle): 
 49          self.handle = handle 
 50          inline = self.handle.readline() 
 51          # zip forward to start of record 
 52          while inline and 'BLASTP' not in inline: 
 53              inline = self.handle.readline() 
 54          self._lookahead = inline 
 55          self._n = 0 
 56          self._in_header = 1 
 57   
 58 -    def next(self): 
 59          self.table_record = BlastTableRec() 
 60          self._n += 1 
 61          inline = self._lookahead 
 62          if not inline: 
 63              return None 
 64          while inline: 
 65              if inline[0] == '#': 
 66                  if self._in_header: 
 67                      self._in_header = self._consume_header(inline) 
 68                  else: 
 69                      break 
 70              else: 
 71                  self._consume_entry(inline) 
 72                  self._in_header = 0 
 73   
 74              inline = self.handle.readline() 
 75          self._lookahead = inline 
 76          self._in_header = 1 
 77          return self.table_record 
 78   
 79 -    def _consume_entry(self, inline): 
 80          current_entry = BlastTableEntry(inline) 
 81          self.table_record.add_entry(current_entry) 
 82   
 83 -    def _consume_header(self, inline): 
 84          for keyword in reader_keywords: 
 85              if keyword in inline: 
 86                  in_header = self._Parse('_parse_%s' % reader_keywords[keyword],inline) 
 87                  break 
 88          return in_header 
 89   
 90 -    def _parse_version(self, inline): 
 91          program, version, date = inline.split()[1:] 
 92          self.table_record.program = program 
 93          self.table_record.version = version 
 94          self.table_record.date = date 
 95          return 1 
 96   
 97 -    def _parse_iteration(self, inline): 
 98          self.table_record.iteration = int(inline.split()[2]) 
 99          return 1 
100   
101 -    def _parse_query(self, inline): 
102          self.table_record.query = inline.split()[2:] 
103          return 1 
104   
105 -    def _parse_database(self, inline): 
106          self.table_record.database = inline.split()[2] 
107          return 1 
108   
109 -    def _parse_fields(self, inline): 
110          return 0 
111   
112 -    def _Parse(self, method_name, inline): 
113          return getattr(self,method_name)(inline) 
114