Source Code for Module Bio.Affy.CelFile

 1  # Copyright 2004 by Harry Zuzan.  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  Classes for accessing the information in Affymetrix cel files. 
 8   
 9  Functions: 
10  read      Read a cel file and store its contents in a Record 
11   
12  Classes: 
13  Record    Contains the information from a cel file 
14  """ 
15   
16  import numpy 
17   
18   
19 -class Record(object): 
20      """ 
21      Stores the information in a cel file 
22      """ 
23 -    def __init__(self): 
24          self.intensities = None 
25          self.stdevs = None 
26          self.npix = None 
27          self.nrows = None 
28          self.ncols = None 
29   
30   
31 -def read(handle): 
32      """ 
33      Read the information in a cel file, and store it in a Record. 
34      """ 
35      # Needs error handling. 
36      # Needs to know the chip design. 
37      record = Record() 
38      section = "" 
39      for line in handle: 
40          if not line.strip(): 
41              continue 
42          if line[:8] == "[HEADER]": 
43              section = "HEADER" 
44          elif line[:11] == "[INTENSITY]": 
45              section = "INTENSITY" 
46              record.intensities = numpy.zeros((record.nrows, record.ncols)) 
47              record.stdevs = numpy.zeros((record.nrows, record.ncols)) 
48              record.npix = numpy.zeros((record.nrows, record.ncols), int) 
49          elif line[0] == "[": 
50              section = "" 
51          elif section == "HEADER": 
52              keyword, value = line.split("=", 1) 
53              if keyword == "Cols": 
54                  record.ncols = int(value) 
55              elif keyword == "Rows": 
56                  record.nrows = int(value) 
57          elif section == "INTENSITY": 
58              if "=" in line: 
59                  continue 
60              words = line.split() 
61              y, x = map(int, words[:2]) 
62              record.intensities[x, y] = float(words[2]) 
63              record.stdevs[x, y] = float(words[3]) 
64              record.npix[x, y] = int(words[4]) 
65      return record 
66