/usr/share/pyshared/Bio/Affy/CelFile.py is in python-biopython 1.58-1.
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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Classes for accessing the information in Affymetrix cel files.
Functions:
read Read a cel file and store its contents in a Record
Classes:
Record Contains the information from a cel file
The following classes are DEPRECATED:
class CelParser: parses cel files
class CelRecord: stores the information from a cel file
"""
import numpy
class Record(object):
"""
Stores the information in a cel file
"""
def __init__(self):
self.intensities = None
self.stdevs = None
self.npix = None
self.nrows = None
self.ncols = None
def read(handle):
"""
Read the information in a cel file, and store it in a Record.
"""
# Needs error handling.
# Needs to know the chip design.
record = Record()
section = ""
for line in handle:
if not line.strip():
continue
if line[:8]=="[HEADER]":
section = "HEADER"
elif line[:11]=="[INTENSITY]":
section = "INTENSITY"
record.intensities = numpy.zeros((record.nrows, record.ncols))
record.stdevs = numpy.zeros((record.nrows, record.ncols))
record.npix = numpy.zeros((record.nrows, record.ncols), int)
elif line[0]=="[":
section = ""
elif section=="HEADER":
keyword, value = line.split("=", 1)
if keyword=="Cols":
record.ncols = int(value)
elif keyword=="Rows":
record.nrows = int(value)
elif section=="INTENSITY":
if "=" in line:
continue
words = line.split()
y, x = map(int, words[:2])
record.intensities[x,y] = float(words[2])
record.stdevs[x,y] = float(words[3])
record.npix[x,y] = int(words[4])
return record
# Everything below is considered deprecated
from Bio.ParserSupport import AbstractConsumer
from numpy import *
class CelScanner(object):
"""Scanner for Affymetrix CEL files (DEPRECATED)
Methods:
feed Feed data into the scanner.
The scanner generates (and calls the consumer) the following
types of events:
Rows - the number of rows on the microarray
Cols - the number of columns on the microarray
StartIntensity - generated when the section [INTENSITY] is found
ReadIntensity - one line in the section [INTENSITY]
This class is DEPRECATED; please use the read() function in this module.
"""
def __init__(self):
import warnings
import Bio
warnings.warn("Bio.Affy.CelFile.CelScanner is deprecated; please use the read() function in this module instead",
Bio.BiopythonDeprecationWarning)
def feed(self, handle, consumer):
"""scanner.feed(handle, consumer)
Feed in a handle to a Cel file for scanning. handle is a file-like
object that contains the Cel file. consumer is a Consumer
object that will receive events as the report is scanned.
"""
section = ""
for line in handle:
if line.strip()=="": continue
if line[0]=="[":
section = ""
if line[:8]=="[HEADER]":
section = "HEADER"
elif line[:11]=="[INTENSITY]":
section = "INTENSITY"
consumer.StartIntensity()
continue
if section=="HEADER":
keyword, value = line.split("=", 1)
if keyword=="Cols": consumer.Cols(value)
if keyword=="Rows": consumer.Rows(value)
continue
elif section=="INTENSITY":
if "=" in line: continue
consumer.ReadIntensity(line)
class CelConsumer(AbstractConsumer):
"""Consumer for Affymetrix CEL files (DEPRECATED)
This class is DEPRECATED; please use the read() function in this module.
"""
def __init__(self):
import warnings
import Bio
warnings.warn("Bio.Affy.CelFile.CelConsumer is deprecated; please use the read() function in this module instead",
Bio.BiopythonDeprecationWarning)
self._mean = None
self._stdev = None
self._npix = None
def Cols(self, value):
self._cols = int(value)
def Rows(self, value):
self._rows = int(value)
def StartIntensity(self):
self._mean = zeros((self._rows, self._cols))
self._stdev = zeros((self._rows, self._cols))
self._npix = zeros((self._rows, self._cols), int)
def ReadIntensity(self, line):
y, x, mean, stdev, npix = map(float, line.split())
x = int(x)
y = int(y)
self._mean[x,y] = mean
self._stdev[x,y] = stdev
self._npix[x,y] = int(npix)
class CelRecord(object):
"""
Stores the information in a cel file (DEPRECATED).
Needs error handling.
Needs to know the chip design.
This class is DEPRECATED; please use the Record class instead.
"""
def __init__(self, data_dict):
"""
Pass the data attributes as a dictionary.
"""
import warnings
import Bio
warnings.warn("Bio.Affy.CelFile.CelRecord is deprecated; please use the read() function in this module instead",
Bio.BiopythonDeprecationWarning)
from copy import deepcopy as dcopy
self._intensities = dcopy(data_dict['intensities'])
self._stdevs = dcopy(data_dict['stdevs'])
self._npix = dcopy(data_dict['npix'])
self._nrows, self._ncols = self._intensities.shape
def intensities(self):
"""
Return a two dimensional array of probe cell intensities.
Dimension 1 -> rows
Dimension 2 -> columns
"""
return self._intensities
def stdevs(self):
"""
Return a two dimensional array of probe cell standard deviations.
Dimension 1 -> rows
Dimension 2 -> columns
"""
return self._stdevs
def npix(self):
"""
Return a two dimensional array of the number of pixels in a probe cell.
Dimension 1 -> rows
Dimension 2 -> columns
"""
return self._npix
def nrows(self):
"""
The number of rows of probe cells in an array.
"""
return self._nrows
def ncols(self):
"""
The number of columns of probe cells in an array.
"""
return self._ncols
def size(self):
"""
The size of the probe cell array as a tuple (nrows,ncols).
"""
return self._nrows, self._ncols
class CelParser(object):
"""
Takes a handle to an Affymetrix cel file, parses the file and
returns an instance of a CelRecord
This class needs error handling.
This class is DEPRECATED; please use the read() function in this module
instead.
"""
def __init__(self, handle=None):
"""
Usually load the class with the cel file (not file name) as
an argument.
"""
import warnings
import Bio
warnings.warn("Bio.Affy.CelFile.CelParser is deprecated; please use the read() function in this module instead",
Bio.BiopythonDeprecationWarning)
self._intensities = None
self._stdevs = None
self._npix = None
if handle is not None: self.parse(handle)
def parse(self, handle):
"""
Takes a handle to a cel file, parses it
and stores it in the three arrays.
There is more information in the cel file that could be retrieved
and stored in CelRecord. The chip type should be a priority.
"""
# (self._intensities, self._stdevs, self._npix) = _cel.parse(data)
scanner = CelScanner()
consumer = CelConsumer()
scanner.feed(handle, consumer)
self._intensities = consumer._mean
self._stdevs = consumer._stdev
self._npix = consumer._npix
self._nrows = self._intensities.shape[0]
self._ncols = self._intensities.shape[1]
def __call__(self):
"""
Returns the parsed data as a CelRecord.
"""
record_dict = {}
record_dict['intensities'] = self._intensities
record_dict['stdevs'] = self._stdevs
record_dict['npix'] = self._npix
return CelRecord(record_dict)
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