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