Source Code for Package Bio.PopGen.FDist

 1  # Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  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   
 7  """ 
 8  This module provides code to work with FDist. 
 9   
10  See http://www.rubic.rdg.ac.uk/~mab/software.html . 
11   
12  Classes: 
13  Record           Holds FDist data. 
14   
15  Functions: 
16  read             Parses a FDist record (file) into a Record object. 
17   
18   
19  """ 
20   
21   
22 -def read(handle): 
23      """Parses FDist data into a Record object. 
24   
25         handle is a file-like object that contains a FDist record. 
26      """ 
27      record = Record() 
28      record.data_org = int(str(handle.next()).rstrip()) 
29      record.num_pops = int(str(handle.next()).rstrip()) 
30      record.num_loci = int(str(handle.next()).rstrip()) 
31      for i in range(record.num_loci): 
32          handle.next() 
33          num_alleles = int(str(handle.next()).rstrip()) 
34          pops_data = [] 
35          if record.data_org==0: 
36              for j in range(record.num_pops): 
37                  line_comp = str(handle.next()).rstrip().split(' ') 
38                  pop_dist = map(lambda x: int(x), line_comp) 
39                  pops_data.append(pop_dist) 
40          else: 
41              raise NotImplementedError('1/alleles by rows not implemented') 
42          record.loci_data.append((num_alleles, pops_data)) 
43      return record 
44   
45   
46 -class Record(object): 
47      """Holds information from a FDist record. 
48   
49      Members: 
50      data_org    Data organization (0 pops by rows, 1 alleles by rows). 
51                  The Record will behave as if data was 0 (converting if needed) 
52   
53      num_pops       Number of populations 
54   
55      num_loci       Number of loci 
56   
57      loci_data      Loci data 
58   
59      loci_data is a list, where each element represents a locus. Each element 
60      is a tuple, the first element is the number of alleles, the second 
61      element a list. Each element of the list is the count of each allele 
62      per population. 
63      """ 
64 -    def __init__(self): 
65          self.data_org    = 0 
66          self.num_pops    = 0 
67          self.num_loci    = 0 
68          self.loci_data   = [] 
69   
70 -    def __str__(self): 
71          rep  = ['0\n']  # We only export in 0 format, even if originally was 1 
72          rep.append(str(self.num_pops) + '\n') 
73          rep.append(str(self.num_loci) + '\n') 
74          rep.append('\n') 
75          for locus_data in self.loci_data: 
76              num_alleles, pops_data = locus_data 
77              rep.append(str(num_alleles) + '\n') 
78              for pop_data in pops_data: 
79                  for allele_count in pop_data: 
80                      rep.append(str(allele_count) + ' ') 
81                  rep.append('\n') 
82              rep.append('\n') 
83          return "".join(rep) 
84