Source Code for Module Bio.Geo.Record

 1  # Copyright 2001 by Katharine Lindner.  All rights reserved. 
 2  # Copyright 2006 by PeterC.  All rights reserved. 
 3  # This code is part of the Biopython distribution and governed by its 
 4  # license.  Please see the LICENSE file that should have been included 
 5  # as part of this package. 
 6   
 7  """ 
 8  Hold GEO data in a straightforward format. 
 9   
10  classes: 
11  o Record - All of the information in an GEO record. 
12   
13  See http://www.ncbi.nlm.nih.gov/geo/ 
14  """ 
15   
16   
17 -class Record(object): 
18      """Hold GEO information in a format similar to the original record. 
19   
20      The Record class is meant to make data easy to get to when you are 
21      just interested in looking at GEO data. 
22   
23      Attributes: 
24      entity_type 
25      entity_id 
26      entity_attributes 
27      col_defs 
28      table_rows 
29   
30      """ 
31 -    def __init__(self): 
32          self.entity_type = '' 
33          self.entity_id = '' 
34          self.entity_attributes = {} 
35          self.col_defs = {} 
36          self.table_rows = [] 
37   
38 -    def __str__( self ): 
39          output = '' 
40          output = output + 'GEO Type: %s\n' % self.entity_type 
41          output = output + 'GEO Id: %s\n' % self.entity_id 
42          att_keys = self.entity_attributes.keys() 
43          att_keys.sort() 
44          for key in att_keys: 
45              contents = self.entity_attributes[ key ] 
46              if isinstance(contents, list): 
47                  for item in contents: 
48                      try: 
49                          output = output + '%s: %s\n' % ( key, item[ :40 ] ) 
50                          output = output + out_block( item[ 40: ] ) 
51                      except: 
52                          pass 
53              elif isinstance(contents, str): 
54                  output = output + '%s: %s\n' % ( key, contents[ :40 ] ) 
55                  output = output + out_block( contents[ 40: ] ) 
56              else: 
57                  print contents 
58                  output = output + '%s: %s\n' % ( key, val[ :40 ] ) 
59                  output = output + out_block( val[ 40: ] ) 
60          col_keys = self.col_defs.keys() 
61          col_keys.sort() 
62          output = output + 'Column Header Definitions\n' 
63          for key in col_keys: 
64              val = self.col_defs[ key ] 
65              output = output + '    %s: %s\n' % ( key, val[ :40 ] ) 
66              output = output + out_block( val[ 40: ], '    ' ) 
67          #May have to display VERY large tables, 
68          #so only show the first 20 lines of data 
69          MAX_ROWS = 20+1 # include header in count 
70          for row in self.table_rows[0:MAX_ROWS]: 
71              output = output + '%s: ' % self.table_rows.index( row ) 
72              for col in row: 
73                  output = output + '%s\t' % col 
74              output = output + '\n' 
75          if len(self.table_rows) > MAX_ROWS: 
76              output = output + '...\n' 
77              row = self.table_rows[-1] 
78              output = output + '%s: ' % self.table_rows.index( row ) 
79              for col in row: 
80                  output = output + '%s\t' % col 
81              output = output + '\n' 
82   
83          return output 
84   
85   
86 -def out_block( text, prefix = '' ): 
87      output = '' 
88      for j in range( 0, len( text ), 80 ): 
89          output = output + '%s%s\n' % ( prefix, text[ j: j + 80 ] ) 
90      output = output + '\n' 
91      return output 
92