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# Copyright 2004 by Harry Zuzan. All rights reserved.
# 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
"""
# We use print in the doctests
from __future__ import print_function
try:
import numpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.Affy.CelFile")
class Record(object):
"""Stores the information in a cel file
Example usage:
>>> from Bio.Affy import CelFile
>>> with open('Affy/affy_v3_example.CEL') as handle:
... c = CelFile.read(handle)
...
>>> print(c.ncols, c.nrows)
5 5
>>> print(c.intensities)
[[ 234. 170. 22177. 164. 22104.]
[ 188. 188. 21871. 168. 21883.]
[ 188. 193. 21455. 198. 21300.]
[ 188. 182. 21438. 188. 20945.]
[ 193. 20370. 174. 20605. 168.]]
>>> print(c.stdevs)
[[ 24. 34.5 2669. 19.7 3661.2]
[ 29.8 29.8 2795.9 67.9 2792.4]
[ 29.8 88.7 2976.5 62. 2914.5]
[ 29.8 76.2 2759.5 49.2 2762. ]
[ 38.8 2611.8 26.6 2810.7 24.1]]
>>> print(c.npix)
[[25 25 25 25 25]
[25 25 25 25 25]
[25 25 25 25 25]
[25 25 25 25 25]
[25 25 25 25 25]]
"""
def __init__(self):
self.version = None
self.GridCornerUL = None
self.GridCornerUR = None
self.GridCornerLR = None
self.GridCornerLL = None
self.DatHeader = None
self.Algorithm = None
self.AlgorithmParameters = None
self.NumberCells = None
self.intensities = None
self.stdevs = None
self.npix = None
self.nrows = None
self.ncols = None
self.nmask = None
self.mask = None
self.noutliers = None
self.outliers = None
self.modified = 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
# Set current section
if line[:5] == "[CEL]":
section = "CEL"
elif 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[:7] == "[MASKS]":
section = "MASKS"
record.mask = numpy.zeros((record.nrows, record.ncols))
elif line[:10] == "[OUTLIERS]":
section = "OUTLIERS"
record.outliers = numpy.zeros((record.nrows, record.ncols))
elif line[:10] == "[MODIFIED]":
section = "MODIFIED"
record.modified = numpy.zeros((record.nrows, record.ncols))
elif line[0] == "[":
# This would be an unknown section
section = ""
elif section == "CEL":
keyword, value = line.split("=", 1)
if keyword == 'Version':
record.version = int(value)
elif section == "HEADER":
# Set record.ncols and record.nrows, remaining data goes into
# record.header dict
keyword, value = line.split("=", 1)
if keyword == "Cols":
record.ncols = int(value)
elif keyword == "Rows":
record.nrows = int(value)
elif keyword == 'GridCornerUL':
x, y = value.split()
record.GridCornerUL = (int(x), int(y))
elif keyword == 'GridCornerUR':
x, y = value.split()
record.GridCornerUR = (int(x), int(y))
elif keyword == 'GridCornerLR':
x, y = value.split()
record.GridCornerLR = (int(x), int(y))
elif keyword == 'GridCornerLL':
x, y = value.split()
record.GridCornerLL = (int(x), int(y))
elif keyword == 'DatHeader':
record.DatHeader = value.strip('\n\r')
elif keyword == 'Algorithm':
record.Algorithm = value.strip('\n\r')
elif keyword == 'AlgorithmParameters':
record.AlgorithmParameters = value.strip('\n\r')
elif section == "INTENSITY":
if "NumberCells" in line:
record.NumberCells = int(line.split("=", 1)[1])
elif "CellHeader" in line:
pass
else:
words = line.split()
y = int(words[0])
x = int(words[1])
record.intensities[x, y] = float(words[2])
record.stdevs[x, y] = float(words[3])
record.npix[x, y] = int(words[4])
elif section == "MASKS":
if "NumberCells" in line:
record.nmask = int(line.split("=", 1)[1])
elif "CellHeader" in line:
pass
else:
words = line.split()
y = int(words[0])
x = int(words[1])
record.mask[x, y] = int(1)
elif section == "OUTLIERS":
if "NumberCells" in line:
record.noutliers = int(line.split("=", 1)[1])
elif "CellHeader" in line:
pass
else:
words = line.split()
y = int(words[0])
x = int(words[1])
record.outliers[x, y] = int(1)
elif section == "MODIFIED":
if "NumberCells" in line:
record.nmodified = int(line.split("=", 1)[1])
elif "CellHeader" in line:
pass
else:
words = line.split()
y = int(words[0])
x = int(words[1])
record.modified[x, y] = float(words[2])
else:
continue
return record
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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