changeset 10:efbf0fde3d03 draft

Deleted selected files

--- a/vcfs2fasta/phe/variant/variant_factory.py	Wed Dec 16 07:25:17 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,92 +0,0 @@
-'''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