First commit.

example.py

@@ -0,0 +1,19 @@
+# coding=utf-8
+
+from table import Table
+
+table = Table(["1", "2", "3"], ["a", "b"], [[1, 2], [3, 4], [5, 6]])
+print "Whole table:"
+print table
+
+print "Just a cell:"
+print table["1", "a"]
+
+print "A row:"
+print table["2", :]
+
+print "A column:"
+print table[:, "b"]
+
+print "A range:"
+print table["2":, :]

setup.py

@@ -0,0 +1,16 @@
+# coding=utf-8
+
+from distutils.core import setup
+from table import __version__ as version
+
+setup(
+    name='table',
+    version=version,
+    py_modules=['table'],
+    url='',
+    license='BSD (2-clause)',
+    author='Eser Aygün',
+    author_email='eser.aygun@gmail.com',
+    description='Provides a two-dimensional table class with named rows and columns, and related I/O utilities.',
+    requires=['numpy']
+)

table.py

@@ -0,0 +1,163 @@
+# coding=utf-8
+
+# Copyright (c) 2012, Eser Aygün
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
+# following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following
+#   disclaimer.
+# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+#   disclaimer in the documentation and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+import numpy
+import csv
+
+__version__ = "0.0.1"
+
+class Table(object):
+    """
+    Provides a two-dimensional matrix with named rows and columns.
+    """
+
+    def __init__(self, rowNames, columnNames, matrix=None):
+        """
+        Creates a table with given row names and column names.
+        Both row names and column names should be unique.
+        The optional matrix argument can be used to initialize the matrix.
+        If provided, the size of the matrix argument should be equal to len(rowNames) * len(columnNames).
+        """
+        self.rowNames = list(rowNames)
+        self.columnNames = list(columnNames)
+        self.rowIndices = dict([(n, i) for i, n in enumerate(self.rowNames)])
+        self.columnIndices = dict([(n, i) for i, n in enumerate(self.columnNames)])
+        self.matrix = numpy.zeros((len(rowNames), len(columnNames)))
+        if matrix is not None:
+            self.matrix[:] = matrix
+
+    def cell(self, rowName, columnName):
+        """
+        Returns the value of the cell on the given row and column.
+        """
+        return self.matrix[self.rowIndices[rowName], self.columnIndices[columnName]]
+
+    def row(self, rowName):
+        """
+        Returns the given row as an array.
+        """
+        return self.matrix[self.rowIndices[rowName], :]
+
+    def column(self, columnName):
+        """
+        Returns the given column as an array.
+        """
+        return self.matrix[:, self.columnIndices[columnName]]
+
+    def __getRowIndex(self, rowName):
+        if rowName is None:
+            return None
+        else:
+            return self.rowIndices[rowName]
+
+    def __getColumnIndex(self, columnName):
+        if columnName is None:
+            return None
+        else:
+            return self.columnIndices[columnName]
+
+    def __getRowSlice(self, rowName):
+        if rowName is None:
+            return None
+        elif isinstance(rowName, slice):
+            return slice(
+                self.__getRowIndex(rowName.start),
+                self.__getRowIndex(rowName.stop),
+                rowName.step
+            )
+        else:
+            return self.__getRowIndex(rowName)
+
+    def __getColumnSlice(self, columnName):
+        if columnName is None:
+            return None
+        elif isinstance(columnName, slice):
+            return slice(
+                self.__getColumnIndex(columnName.start),
+                self.__getColumnIndex(columnName.stop),
+                columnName.step
+            )
+        else:
+            return self.__getColumnIndex(columnName)
+
+    def __getitem__(self, item):
+        if not isinstance(item, tuple) or len(item) != 2:
+            raise ValueError("2-tuple expected")
+
+        return self.matrix[self.__getRowSlice(item[0]), self.__getColumnSlice(item[1])]
+
+    def __setitem__(self, item, value):
+        if not isinstance(item, tuple) or len(item) != 2:
+            raise ValueError("2-tuple expected")
+
+        self.matrix[self.__getRowSlice(item[0]), self.__getColumnSlice(item[1])] = value
+
+    def __repr__(self):
+        return "Table(%s)" % self.matrix
+
+    def __str__(self):
+        return str(self.matrix)
+
+    def __unicode__(self):
+        return unicode(self.matrix)
+
+def readTableFromDelimited(f, separator="\t"):
+    """
+    Reads a table object from given plain delimited file.
+    """
+    rowNames = []
+    columnNames = []
+    matrix = []
+
+    first = True
+    for line in f.readlines():
+        line = line.rstrip()
+        if len(line) == 0:
+            continue
+
+        row = line.split(separator)
+        if first:
+            columnNames = row[1:]
+            first = False
+        else:
+            rowNames.append(row[0])
+            matrix.append([float(c) for c in row[1:]])
+
+    return Table(rowNames, columnNames, matrix)
+
+def readTableFromCSV(f, dialect="excel"):
+    """
+    Reads a table object from given CSV file.
+    """
+    rowNames = []
+    columnNames = []
+    matrix = []
+
+    first = True
+    for row in csv.reader(f, dialect):
+        if first:
+            columnNames = row[1:]
+            first = False
+        else:
+            rowNames.append(row[0])
+            matrix.append([float(c) for c in row[1:]])
+
+    return Table(rowNames, columnNames, matrix)