Source Code for Module Bio.motifs.alignace

 1  # Copyright 2003 by Bartek Wilczynski.  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  """Parsing AlignACE output files 
 7  """ 
 8   
 9  from Bio.motifs import Motif, Instances 
10  from Bio.Alphabet import IUPAC 
11  from Bio.Seq import Seq 
12   
13   
14 -class Record(list): 
15 -    def __init__(self): 
16          self.parameters = None 
17   
18   
19 -def read(handle): 
20      """read(handle)""" 
21      record = Record() 
22      line = handle.next() 
23      record.version = line.strip() 
24      line = handle.next() 
25      record.command = line.strip() 
26      for line in handle: 
27          line = line.strip() 
28          if line=="": 
29              pass 
30          elif line[:4]=="Para": 
31              record.parameters={} 
32          elif line[0]=="#": 
33              seq_name = line.split("\t")[1] 
34              record.sequences.append(seq_name) 
35          elif "=" in line: 
36              par_name, par_value = line.split("=") 
37              par_name = par_name.strip() 
38              par_value = par_value.strip() 
39              record.parameters[par_name]=par_value 
40          elif line[:5]=="Input": 
41              record.sequences=[] 
42          elif line[:5]=="Motif": 
43              words = line.split() 
44              assert words[0]=="Motif" 
45              number = int(words[1]) 
46              instances = [] 
47          elif line[:3]=="MAP": 
48              alphabet = IUPAC.unambiguous_dna 
49              instances = Instances(instances, alphabet) 
50              motif = Motif(alphabet, instances) 
51              motif.score = float(line.split()[-1]) 
52              motif.number = number 
53              motif.mask = mask 
54              record.append(motif) 
55          elif len(line.split("\t"))==4: 
56              seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna) 
57              instances.append(seq) 
58          elif "*" in line: 
59              mask = line.strip("\r\n") 
60          else: 
61              raise ValueError(line) 
62      return record 
63