Source Code for Package Bio.Geo

 1  # Copyright 2001 by Katharine Lindner.  All rights reserved. 
 2  # Copyright 2006 by PeterC.  All rights reserved. 
 3  # Copyright 2007 by Michiel de Hoon.  All rights reserved. 
 4  # This code is part of the Biopython distribution and governed by its 
 5  # license.  Please see the LICENSE file that should have been included 
 6  # as part of this package. 
 7  """Parser for files from NCBI's Gene Expression Omnibus (GEO). 
 8   
 9  http://www.ncbi.nlm.nih.gov/geo/ 
10  """ 
11   
12  import Record 
13   
14   
15 -def _read_key_value(line): 
16      words = line[1:].split("=", 1) 
17      try: 
18          key, value = words 
19          value = value.strip() 
20      except ValueError: 
21          key = words[0] 
22          value = "" 
23      key = key.strip() 
24      return key, value 
25   
26   
27 -def parse(handle): 
28      record = None 
29      for line in handle: 
30          line = line.strip('\n').strip('\r') 
31          if not line: 
32              continue # Ignore empty lines 
33          c = line[0] 
34          if c=='^': 
35              if record: 
36                  yield record 
37              record = Record.Record() 
38              record.entity_type, record.entity_id = _read_key_value(line) 
39          elif c=='!': 
40              if line in ('!Sample_table_begin', 
41                          '!Sample_table_end', 
42                          '!Platform_table_begin', 
43                          '!Platform_table_end'): 
44                  continue 
45              key, value = _read_key_value(line) 
46              if key in record.entity_attributes: 
47                  if type(record.entity_attributes[key])==list: 
48                      record.entity_attributes[key].append(value) 
49                  else: 
50                      existing = record.entity_attributes[key] 
51                      record.entity_attributes[key] = [existing, value] 
52              else: 
53                  record.entity_attributes[key] = value 
54          elif c=='#': 
55              key, value = _read_key_value(line) 
56              assert key not in record.col_defs 
57              record.col_defs[key] = value 
58          else: 
59              row = line.split("\t") 
60              record.table_rows.append(row) 
61      yield record 
62