Now provides duan et al sample dataset

MANIFEST.in

@@ -1 +1,2 @@
 recursive-include iced *.c *.h *.py
+recursive-include *.matrix *.bed

iced/datasets/__init__.py

@@ -0,0 +1,2 @@
+from .base import clear_data_home, get_data_home
+from .base import load_sample_yeast

iced/datasets/base.py

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+import os
+from os import environ, makedirs
+from os.path import join, expanduser, exists
+from os.path import dirname
+import shutil
+
+from iced import io
+
+# authors: Nelle Varoquaux <[email protected]>
+
+# This module is greatly inspired from sklearn.datasets
+
+
+def get_data_home(data_home=None):
+    """Return the path of the scikit-learn data dir.
+
+    This folder is used by some large dataset loaders to avoid
+    downloading the data several times.
+
+    By default the data dir is set to a folder named 'scikit_learn_data'
+    in the user home folder.
+
+    Alternatively, it can be set by the 'SCIKIT_LEARN_DATA' environment
+    variable or programmatically by giving an explicit folder path. The
+    '~' symbol is expanded to the user home folder.
+
+    If the folder does not already exist, it is automatically created.
+    """
+    if data_home is None:
+        data_home = environ.get('HICLIB_DATA',
+                                join('~', 'hiclib_data'))
+    data_home = expanduser(data_home)
+    if not exists(data_home):
+        makedirs(data_home)
+    return data_home
+
+
+def clear_data_home(data_home=None):
+    """Delete all the content of the data home cache."""
+    data_home = get_data_home(data_home)
+    shutil.rmtree(data_home)
+
+
+def load_sample_yeast():
+    """
+    Load and return a sample of S. cerevisiae contact count matrix from duan
+    et al, Nature, 2009
+
+    Returns:
+        counts, lengths:
+            tuple of two elements, the first a contact count matrix, the
+            second an ndarray containing the lengths of the chromosomes.
+    """
+    module_path = dirname(__file__)
+    lengths = io.load_lengths(
+        os.path.join(module_path, "data/duan2009/duan.SC.10000.raw_sub.bed"))
+    counts = io.load_counts(
+        os.path.join(module_path,
+                     "data/duan2009/duan.SC.10000.raw_sub.matrix"),
+        lengths=lengths)
+    counts = counts.toarray()
+    counts = counts.T + counts
+    return counts, lengths