Source Code for Module biana.BianaObjects.BlastResult

  1  import re 
  2  import sys 
  3   
  4 -class BlastResult(object): 
  5      """ 
  6      Object to store blast results 
  7   
  8      All values are relative to absolute sequence position, starting at index 1!!! 
  9      """ 
 10   
 11 -    def __init__(self, method, mode): 
 12   
 13          self.sequenceID_A = None 
 14          self.sequenceID_B = None 
 15          self.e_value = None 
 16          self.align_length = None 
 17          self.score = None 
 18          self.score_bits = None 
 19          self.identities = None 
 20          self.positives = None 
 21          self.gaps = 0 
 22          self.query_start = None 
 23          self.query_end = None 
 24          self.query_length = None 
 25          self.sbjct_start = None 
 26          self.sbjct_end = None 
 27          self.sbjct_length = None 
 28          self.method = method 
 29          self.mode = mode 
 30          self.query_coverage = None 
 31          self.sbjct_coverage = None 
 32          self.query_exact_match_list = [] 
 33          self.sbjct_exact_match_list = [] 
 34          self.query_similar_match_list = [] 
 35          self.sbjct_similar_match_list = [] 
 36   
 37 -    def __repr__(self): 
 38          return self.__str__() 
 39   
 40 -    def __str__(self): 
 41   
 42          return "%s\n" %"\t".join(["%s" %self.sequenceID_A, 
 43                                    "%s" %self.sequenceID_B, 
 44                                    "%s" %self.e_value, 
 45                                    "%s" %self.score, 
 46                                    "%s" %self.score_bits, 
 47                                    "%s" %self.query_start, 
 48                                    "%s" %self.query_end, 
 49                                    "%s" %self.sbjct_start, 
 50                                    "%s" %self.sbjct_end, 
 51                                    "%s" %self.identities, 
 52                                    "%s" %self.positives, 
 53                                    "%s" %self.gaps, 
 54                                    "%s" %self.method, 
 55                                    "%s" %self.mode, 
 56                                    "%s" %self.get_query_coverage(), 
 57                                    "%s" %self.get_sbjct_coverage()]) 
 58   
 59   
 60 -    def get_query_coverage(self): 
 61          if self.query_coverage is None: 
 62              if self.query_length is None: 
 63                  sys.stderr.write("Impossible to calculate query coverage: length not known. Query %s Subjct %s\n" %(self.sequenceID_A,self.sequenceID_B)) 
 64                  sys.exit(1) 
 65                  return 0 
 66              self.query_coverage = (int(self.query_end)-int(self.query_start))*100/float(self.query_length) 
 67          return self.query_coverage 
 68   
 69 -    def get_sbjct_coverage(self): 
 70          if self.sbjct_coverage is None: 
 71              if self.sbjct_length is None: 
 72                  sys.stderr.write("Impossible to calculate query coverage: length not known. Sbjct: %s\n"%self.sequenceID_B) 
 73                  return 0 
 74              self.sbjct_coverage = (int(self.sbjct_end)-int(self.sbjct_start))*100/float(self.sbjct_length) 
 75          return self.sbjct_coverage 
 76   
 77 -    def set_evalue(self, e_value): 
 78          if re.search("^e",e_value): 
 79              self.e_value = float("1"+e_value) 
 80          else: 
 81              self.e_value = float(e_value) 
 82   
 83 -    def write(self, fd_out): 
 84          fd_out.write(self.__str__()) 
 85           
 86 -    def reset(self): 
 87   
 88          self.e_value = None 
 89          self.align_length = None 
 90          self.score = None 
 91          self.score_bits = None 
 92          self.identities = None 
 93          self.positives = None 
 94          self.gaps = 0 
 95          self.query_start = None 
 96          self.query_end = None 
 97          self.sbjct_start = None 
 98          self.sbjct_end = None 
 99          self.query_coverage = None 
100          self.sbjct_coverage = None 
101   
102           
103          self.query_exact_match_list = [] 
104          self.sbjct_exact_match_list = [] 
105          self.query_similar_match_list = [] 
106          self.sbjct_similar_match_list = [] 
107