Merge branch 'develop'

gopca/__init__.py

@@ -5,12 +5,13 @@
 import pkg_resources
 
 from .params import GOPCAParams
+from .config import GOPCAConfig
 from .signature import GOPCASignature
 from .signature_matrix import GOPCASignatureMatrix
 from .run import GOPCARun
 from .go_pca import GOPCA
 
 version = text(pkg_resources.require('gopca')[0].version)
 
-__all__ = ['GOPCAParams', 'GOPCA', 'GOPCARun',
+__all__ = ['GOPCAParams', 'GOPCAConfig', 'GOPCA', 'GOPCARun',
            'GOPCASignatureMatrix', 'GOPCASignature']

gopca/cli/print_info.py

@@ -107,7 +107,7 @@ def main(args=None):
     if run is not None:
         print('GO-PCA Run')
         print('----------')
-        print('- GO-PCA version: %s' % run.version)
+        print('- GO-PCA version: %s' % run.gopca_version)
         print('- Timestamp: %s' % run.timestamp)
         print('- Exec. time: %.1f s' % run.exec_time)
 

gopca/config.py

@@ -0,0 +1,140 @@
+# Copyright (c) 2016 Florian Wagner
+#
+# This file is part of GO-PCA.
+#
+# GO-PCA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License, Version 3,
+# as published by the Free Software Foundation.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+"""Module containing the `GOPCAConfig` class.
+
+"""
+
+from __future__ import (absolute_import, division,
+                        print_function, unicode_literals)
+from builtins import *
+
+import logging
+import hashlib
+import copy
+
+from genometools.basic import GeneSetCollection
+from genometools.ontology import GeneOntology
+from . import GOPCAParams
+
+logger = logging.getLogger(__name__)
+
+
+class GOPCAConfig(object):
+    """A GO-PCA configuration.
+
+    This class represents a complete set of inputs to the GO-PCA algorithm,
+    excluding the expression data. Specifically, the inputs consist of
+    parameter settings, represented by the `GOPCAParams` class, as well as a
+    list of gene sets (optionally including Gene Ontology data; represented by
+    the `GOPCAGeneSets` class).
+
+    Furthermore, two versions of the parameter settings are stored: The
+    first version (`user_params`) holds the values exactly as specified by the
+    user. Some of those values can have special meaning, such as ``-1`` for the
+    XL-mHG ``L`` parameter (``mHG_L``), which will be automatically converted
+    to ``p/8`` (where ``p`` is the number of genes). The second version
+    (simply called `params`) holds the values actually used by the algorithm.
+    So in the previous example, the ``mHG_L`` parameter stored in this version
+    would equal ``p/8`` (rounded down to the nearest integer).
+
+    Parameters
+    ----------
+    user_params: `GOPCAParams`
+        See :attr:`user_params` attribute.
+    gene_sets: `genometools.basic.GeneSetCollection`
+        See :attr:`gene_set_coll` attribute.
+    gene_ontology: `genometools.ontology.GeneOntology`, optional
+        See :attr:`gene_ontology` attribute.
+    params: `GOPCAParams`, optional
+        See :attr:`params` attribute.
+
+    Attributes
+    ----------
+    user_params: `GOPCAParams`
+        The GO-PCA parameter settings, as specified by the user.
+    gene_sets: `genometools.basic.GeneSetCollection`
+        The list of gene sets to be used by GO-PCA.
+    gene_ontology: `genometools.ontology.GeneOntology` or None
+        The Gene Ontology (only if gene sets are based on GO annotations.)
+    params: `GOPCAParams` or None
+        The final GO-PCA parameter settings, after resolving parameter values
+        with special meanings (see above).
+    """
+    def __init__(self, user_params, gene_sets,
+                 gene_ontology=None, params=None):
+
+        # store configuration
+        assert isinstance(user_params, GOPCAParams)
+        assert isinstance(gene_sets, GeneSetCollection)
+
+        if gene_ontology is not None:
+            assert isinstance(gene_ontology, GeneOntology)
+
+        if params is not None:
+            assert isinstance(params, GOPCAParams)
+
+        self.user_params = user_params
+        self.params = params
+        self.gene_sets = gene_sets
+        self.gene_ontology = gene_ontology
+
+    def __repr__(self):
+        return '<%s instance (hash="%s")>' % \
+               (self.__class__.__name__, self.hash)
+
+    def __str__(self):
+        return '<%s instance (hash="%s")>' % \
+               (self.__class__.__name__, self.hash)
+
+    def __eq__(self, other):
+        if self is other:
+            return True
+        elif type(self) is type(other):
+            return self.__dict__ == other.__dict__
+        else:
+            return NotImplemented
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    @property
+    def hash(self):
+        data_str = ';'.join(
+            repr(v) for v in [self.user_params, self.params,
+                              self.gene_sets, self.gene_ontology])
+        data = data_str.encode('UTF-8')
+        return str(hashlib.md5(data).hexdigest())
+
+    def finalize_params(self, num_genes):
+        """Replace parameters set to special values with final value.
+
+        Parameters
+        ----------
+        num_genes: int
+            The number of genes in the analysis.
+        """
+        params = copy.deepcopy(self.user_params)
+
+        # determine mHG_L, if -1 or 0
+        if params.mHG_L == -1:
+            # -1 = determine L automatically => p / 8
+            params.set_param('mHG_L', int(num_genes / 8.0))
+        elif params.mHG_L == 0:
+            # 0 = "disable" effect of L => set it to the number of genes
+            params.set_param('mHG_L', num_genes)
+
+        self.params = params