Source Code for Module Bio.Emboss.PrimerSearch

 1  """Code to interact with the primersearch program from EMBOSS. 
 2  """ 
 3   
 4   
 5 -class InputRecord(object): 
 6      """Represent the input file into the primersearch program. 
 7   
 8      This makes it easy to add primer information and write it out to the 
 9      simple primer file format. 
10      """ 
11 -    def __init__(self): 
12          self.primer_info = [] 
13   
14 -    def __str__(self): 
15          output = "" 
16          for name, primer1, primer2 in self.primer_info: 
17              output += "%s %s %s\n" % (name, primer1, primer2) 
18          return output 
19   
20 -    def add_primer_set(self, primer_name, first_primer_seq, 
21                         second_primer_seq): 
22          """Add primer information to the record. 
23          """ 
24          self.primer_info.append((primer_name, first_primer_seq, 
25                                   second_primer_seq)) 
26   
27   
28 -class OutputRecord(object): 
29      """Represent the information from a primersearch job. 
30   
31      amplifiers is a dictionary where the keys are the primer names and 
32      the values are a list of PrimerSearchAmplifier objects. 
33      """ 
34 -    def __init__(self): 
35          self.amplifiers = {} 
36   
37   
38 -class Amplifier(object): 
39      """Represent a single amplification from a primer. 
40      """ 
41 -    def __init__(self): 
42          self.hit_info = "" 
43          self.length = 0 
44   
45   
46 -def read(handle): 
47      """Get output from primersearch into a PrimerSearchOutputRecord 
48      """ 
49      record = OutputRecord() 
50   
51      for line in handle: 
52          if not line.strip(): 
53              continue 
54          elif line.startswith("Primer name"): 
55              name = line.split()[-1] 
56              record.amplifiers[name] = [] 
57          elif line.startswith("Amplimer"): 
58              amplifier = Amplifier() 
59              record.amplifiers[name].append(amplifier) 
60          elif line.startswith("\tSequence: "): 
61              amplifier.hit_info = line.replace("\tSequence: ", "") 
62          elif line.startswith("\tAmplimer length: "): 
63              length = line.split()[-2] 
64              amplifier.length = int(length) 
65          else: 
66              amplifier.hit_info += line 
67   
68      for name in record.amplifiers: 
69          for amplifier in record.amplifiers[name]: 
70              amplifier.hit_info = amplifier.hit_info.rstrip() 
71   
72      return record 
73