Source Code for Module Bio.PopGen.GenePop.LargeFileParser

  1  # Copyright 2010 by Tiago Antao.  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  Large file parsing of Genepop files 
  8   
  9  The standard parser loads the whole file into memory. This parser 
 10  provides an iterator over data. 
 11   
 12  Classes: 
 13  LargeRecord           Holds GenePop data. 
 14   
 15  Functions: 
 16  read             Parses a GenePop record (file) into a Record object. 
 17   
 18  """ 
 19   
 20   
 21 -def get_indiv(line): 
 22      indiv_name, marker_line = line.split(',') 
 23      markers = marker_line.replace('\t', ' ').split(' ') 
 24      markers = [marker for marker in markers if marker!=''] 
 25      if len(markers[0]) in [2, 4]:  # 2 digits per allele 
 26          marker_len = 2 
 27      else: 
 28          marker_len = 3 
 29      try: 
 30          allele_list = [(int(marker[0:marker_len]), 
 31                         int(marker[marker_len:])) 
 32                     for marker in markers] 
 33      except ValueError:  # Haploid 
 34          allele_list = [(int(marker[0:marker_len]),) 
 35                     for marker in markers] 
 36      return indiv_name, allele_list, marker_len 
 37   
 38   
 39 -def read(handle): 
 40      """Parses a handle containing a GenePop file. 
 41   
 42         handle is a file-like object that contains a GenePop record. 
 43      """ 
 44      record = Record(handle) 
 45      record.comment_line = str(handle.readline()).rstrip() 
 46      #We can now have one loci per line or all loci in a single line 
 47      #separated by either space or comma+space... 
 48      #We will remove all commas on loci... that should not be a problem 
 49      sample_loci_line = str(handle.readline()).rstrip().replace(',', '') 
 50      all_loci = sample_loci_line.split(' ') 
 51      record.loci_list.extend(all_loci) 
 52      line = handle.readline() 
 53      while line!="": 
 54          line = line.rstrip() 
 55          if line.upper()=="POP": 
 56              record.stack.append("POP") 
 57              break 
 58          record.loci_list.append(line) 
 59          line = handle.readline() 
 60      next_line = handle.readline().rstrip() 
 61      indiv_name, allele_list, record.marker_len = get_indiv(next_line) 
 62      record.stack.append(next_line) 
 63      return record 
 64   
 65   
 66 -class Record(object): 
 67      """Holds information from a GenePop record. 
 68   
 69      Members: 
 70      marker_len         The marker length (2 or 3 digit code per allele). 
 71   
 72      comment_line       Comment line. 
 73   
 74      loci_list          List of loci names. 
 75   
 76      data_generator     Iterates over population data. 
 77   
 78      The generator will only work once. If you want to read a handle 
 79      twice you have to re-open it! 
 80   
 81      data_generator can either be () - an empty tuple - marking a new 
 82      population or an individual. An individual is something like 
 83      ('Ind1', [(1,1), (3,None), (200,201)], 
 84      In the case above the individual is called Ind1, 
 85      has three diploid loci. For the second loci, one of the alleles 
 86      is unknown. 
 87   
 88      """ 
 89 -    def __init__(self, handle): 
 90          self.handle = handle 
 91          self.marker_len = 0 
 92          self.comment_line = "" 
 93          self.loci_list = [] 
 94          self.populations = [] 
 95          self.data_generator = None 
 96          self.stack = [] 
 97   
 98 -    def data_generator(self): 
 99          for handle in [self.stack, self.handle]: 
100              for line in handle: 
101                  line = line.rstrip() 
102                  if line.upper()=='POP': 
103                      yield () 
104                  else: 
105                      indiv_name, allele_list, marker_len = get_indiv(line) 
106                      clean_list = [] 
107                      for locus in allele_list: 
108                          mk_real = [] 
109                          for al in locus: 
110                              if al==0: 
111                                  mk_real.append(None) 
112                              else: 
113                                  mk_real.append(al) 
114                          clean_list.append(tuple(mk_real)) 
115                      yield indiv_name, clean_list 
116          raise StopIteration() 
117