diff phe/variant/variant_factory.py @ 22:96f393ad7fc6 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/variant_factory.py	Wed Dec 23 04:50:58 2015 -0500
@@ -0,0 +1,92 @@
+'''Classes and functions for working with variant callers.
+
+Created on 22 Sep 2015
+
+@author: alex
+'''
+import glob
+import inspect
+import logging
+import os
+import sys
+
+from phe.variant import VariantCaller
+
+def dynamic_caller_loader():
+    """Fancy way of dynamically importing existing variant callers.
+    
+    Returns
+    -------
+    dict:
+        Available variant callers dictionary. Keys are parameters that
+        can be used to call variants.
+    """
+
+    # We assume the caller are in the same directory as THIS file.
+    variants_dir = os.path.dirname(__file__)
+    variants_dir = os.path.abspath(variants_dir)
+
+    # This is populated when the module is first imported.
+    avail_callers = {}
+
+    # Add this directory to the syspath.
+    sys.path.insert(0, variants_dir)
+
+    # Find all "py" files.
+    for caller_mod in glob.glob(os.path.join(variants_dir, "*.py")):
+
+        # Derive name of the module where caller is.
+        caller_mod_file = os.path.basename(caller_mod)
+
+        # Ignore __init__ file, only base class is there.
+        if caller_mod_file.startswith("__init__"):
+            continue
+
+        # Import the module with a caller.
+        mod = __import__(caller_mod_file.replace(".pyc", "").replace(".py", ""))
+
+        # Find all the classes contained in this module.
+        classes = inspect.getmembers(mod, inspect.isclass)
+        for cls_name, cls in classes:
+            # For each class, if it is a sublass of VariantCaller, add it.
+            if cls_name != "VariantCaller" and issubclass(cls, VariantCaller):
+                # The name is inherited and defined within each caller.
+                avail_callers[cls.name] = cls
+
+    sys.path.remove(variants_dir)
+
+    return avail_callers
+
+_avail_variant_callers = dynamic_caller_loader()
+
+def available_callers():
+    """Return list of available variant callers."""
+    return _avail_variant_callers.keys()
+
+def factory(variant=None, custom_options=None):
+    """Make an instance of a variant class.
+    
+    Parameters:
+    -----------
+    variant: str, optional
+        Name of the variant class to instantiate.
+    custom_options: str, optional
+        Custom options to be passed directly to the implementing class.
+    
+    Returns:
+    --------
+    :py:class:`phe.variant.VariantCaller`:
+        Instance of the :py:class:`phe.variant.VariantCaller` for given
+        variant name, or None if one couldn't be found.
+    """
+    if variant is not None and isinstance(variant, str):
+
+        variant = variant.lower()
+        if variant in _avail_variant_callers:
+            return _avail_variant_callers[variant](cmd_options=custom_options)
+        else:
+            logging.error("No implementation for %s mapper.")
+            return None
+
+    logging.warn("Unknown parameters. Mapper could not be initialised.")
+    return None