Bundle BioPython code so that installation is not necessary (Tests an…

…d documentation directories have been removed)

Bio/Affy/CelFile.py

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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")
+
+__docformat__ = "restructuredtext en"
+
+
+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()

Bio/Affy/__init__.py

@@ -0,0 +1,9 @@
+# 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.
+#
+
+"""Deal with Affymetrix related data such as cel files.
+"""
+
+__docformat__ = "restructuredtext en"