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comparison phe/variant/variant_factory.py @ 16:1d0bc21232ec draft

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author ulfschaefer
date Wed, 16 Dec 2015 07:32:22 -0500
parents f72039c5faa4
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15:fd42dbe82c12 16:1d0bc21232ec
1 '''Classes and functions for working with variant callers.
2
3 Created on 22 Sep 2015
4
5 @author: alex
6 '''
7 import glob
8 import inspect
9 import logging
10 import os
11 import sys
12
13 from phe.variant import VariantCaller
14
15 def dynamic_caller_loader():
16 """Fancy way of dynamically importing existing variant callers.
17
18 Returns
19 -------
20 dict:
21 Available variant callers dictionary. Keys are parameters that
22 can be used to call variants.
23 """
24
25 # We assume the caller are in the same directory as THIS file.
26 variants_dir = os.path.dirname(__file__)
27 variants_dir = os.path.abspath(variants_dir)
28
29 # This is populated when the module is first imported.
30 avail_callers = {}
31
32 # Add this directory to the syspath.
33 sys.path.insert(0, variants_dir)
34
35 # Find all "py" files.
36 for caller_mod in glob.glob(os.path.join(variants_dir, "*.py")):
37
38 # Derive name of the module where caller is.
39 caller_mod_file = os.path.basename(caller_mod)
40
41 # Ignore __init__ file, only base class is there.
42 if caller_mod_file.startswith("__init__"):
43 continue
44
45 # Import the module with a caller.
46 mod = __import__(caller_mod_file.replace(".pyc", "").replace(".py", ""))
47
48 # Find all the classes contained in this module.
49 classes = inspect.getmembers(mod, inspect.isclass)
50 for cls_name, cls in classes:
51 # For each class, if it is a sublass of VariantCaller, add it.
52 if cls_name != "VariantCaller" and issubclass(cls, VariantCaller):
53 # The name is inherited and defined within each caller.
54 avail_callers[cls.name] = cls
55
56 sys.path.remove(variants_dir)
57
58 return avail_callers
59
60 _avail_variant_callers = dynamic_caller_loader()
61
62 def available_callers():
63 """Return list of available variant callers."""
64 return _avail_variant_callers.keys()
65
66 def factory(variant=None, custom_options=None):
67 """Make an instance of a variant class.
68
69 Parameters:
70 -----------
71 variant: str, optional
72 Name of the variant class to instantiate.
73 custom_options: str, optional
74 Custom options to be passed directly to the implementing class.
75
76 Returns:
77 --------
78 :py:class:`phe.variant.VariantCaller`:
79 Instance of the :py:class:`phe.variant.VariantCaller` for given
80 variant name, or None if one couldn't be found.
81 """
82 if variant is not None and isinstance(variant, str):
83
84 variant = variant.lower()
85 if variant in _avail_variant_callers:
86 return _avail_variant_callers[variant](cmd_options=custom_options)
87 else:
88 logging.error("No implementation for %s mapper.")
89 return None
90
91 logging.warn("Unknown parameters. Mapper could not be initialised.")
92 return None