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I/O caching now automatic without hard-coded modules
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Felix Simkovic committed Jun 20, 2017
1 parent 0d82fe6 commit 3c45d37
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Showing 2 changed files with 50 additions and 34 deletions.
78 changes: 47 additions & 31 deletions conkit/io/_cache.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,14 @@
__date__ = '19 Jun 2017'
__version__ = "1.0"

import copy
import glob
import importlib
import os
import re

RE_CLASS_DECLARATION = re.compile("^class\s+([A-Za-z0-9]+)\s*(.*):$")


class _CacheObj(object):
"""Container for individual module"""
Expand All @@ -55,13 +63,25 @@ def __init__(self, id, module, object, group):
self.object = object
self.group = group

def __repr__(self):
return "{name}(id={id} module={module} object={object} group={group}".format(
name=self.__class__.__name__, **{k: getattr(self, k) for k in self.__class__.__slots__}
)


class _ParserCache(object):
"""Cache to hold handlers to each file parser"""

# This mask is for backward-compatibility and extensions to avoid re-writing the same algorithms
MASKS = {
"a3m": ["a3m", "a3m-inserts"],
"casp": ["casp", "casprr"],
"pcons": ["pconsc", "pconsc2", "pconsc3"],
"psicov": ["psicov", "metapsicov"]
}

def __init__(self):
self._cfile_parsers = [] # Contact file parsers
self._sfile_parsers = [] # Sequence file parsers
self._parsers = []

self.__construct()

Expand All @@ -80,48 +100,44 @@ def __repr__(self):
def contact_file_parsers(self):
"""A dict of contact file parsers"""
# Mask as dictionaries to not break existing code
return {c.id: c for c in self._cfile_parsers}
return {c.id: c for c in self._parsers if c.group == "_ContactFileParser" or c.group == "_GenericStructureParser"}

@property
def sequence_file_parsers(self):
"""A dict of sequence file parsers"""
# Mask as dictionaries to not break existing code
return {c.id: c for c in self._sfile_parsers}
return {c.id: c for c in self._parsers if c.group == "_SequenceFileParser"}

@property
def file_parsers(self):
"""A dict of all file parsers"""
# Mask as dictionaries to not break existing code
return {c.id: c for c in self._sfile_parsers + self._cfile_parsers}
return {c.id: c for c in self._parsers}

def __construct(self):
"""Create the handles"""
base = "conkit.io."

self._cfile_parsers += [_CacheObj("bclcontact", base + "bclcontact", "BCLContactParser", "contact")]
self._cfile_parsers += [_CacheObj("bbcontacts", base + "bbcontacts", "BbcontactsParser", "contact")]
self._cfile_parsers += [_CacheObj("ccmpred", base + "ccmpred", "CCMpredParser", "contact")]
self._cfile_parsers += [_CacheObj("casprr", base + "casp", "CaspParser", "contact")]
self._cfile_parsers += [_CacheObj("comsat", base + "comsat", "ComsatParser", "contact")]
self._cfile_parsers += [_CacheObj("epcmap", base + "epcmap", "EPCMapParser", "contact")]
self._cfile_parsers += [_CacheObj("evfold", base + "evfold", "EVfoldParser", "contact")]
self._cfile_parsers += [_CacheObj("freecontact", base + "freecontact", "FreeContactParser", "contact")]
self._cfile_parsers += [_CacheObj("gremlin", base + "gremlin", "GremlinParser", "contact")]
self._cfile_parsers += [_CacheObj("membrain", base + "membrain", "MemBrainParser", "contact")]
self._cfile_parsers += [_CacheObj("pconsc", base + "pcons", "PconsParser", "contact")]
self._cfile_parsers += [_CacheObj("pconsc2", base + "pcons", "PconsParser", "contact")]
self._cfile_parsers += [_CacheObj("pconsc3", base + "pcons", "PconsParser", "contact")]
self._cfile_parsers += [_CacheObj("pdb", base + "pdb", "PdbParser", "contact")]
self._cfile_parsers += [_CacheObj("mmcif", base + "pdb", "MmCifParser", "contact")]
self._cfile_parsers += [_CacheObj("plmdca", base + "plmdca", "PlmDCAParser", "contact")]
self._cfile_parsers += [_CacheObj("psicov", base + "psicov", "PsicovParser", "contact")]
self._cfile_parsers += [_CacheObj("metapsicov", base + "psicov", "PsicovParser", "contact")]

self._sfile_parsers += [_CacheObj("a3m", base + "a3m", "A3mParser", "sequence")]
self._sfile_parsers += [_CacheObj("a3m-inserts", base + "a3m", "A3mParser", "sequence")]
self._sfile_parsers += [_CacheObj("fasta", base + "fasta", "FastaParser", "sequence")]
self._sfile_parsers += [_CacheObj("jones", base + "jones", "JonesParser", "sequence")]
self._sfile_parsers += [_CacheObj("stockholm", base + "stockholm", "StockholmParser", "sequence")]
path = os.path.abspath(os.path.dirname(__file__))
for m in glob.glob(os.path.join(path, "[!_]*.py")):
with open(m, "r") as f_in:
lines = [RE_CLASS_DECLARATION.match(l.strip()) for l in f_in if RE_CLASS_DECLARATION.match(l.strip())]
for match in lines:
decl = _CacheObj(None, None, match.group(1), None)
ggroup = match.group(2)
if ggroup and ggroup.startswith("(") and ggroup.endswith(")"):
decl.group = ggroup.replace("(", "").replace(")", "")
else:
decl.group = "Ungrouped"
name = os.path.basename(m).replace(".py", "")
decl.module = "conkit.io." + name
objname = decl.object.lower().replace("parser", "")
if objname in _ParserCache.MASKS:
for extra in _ParserCache.MASKS[objname]:
decl_ = copy.copy(decl)
decl_.id = extra
self._parsers += [decl_]
else:
decl.id = objname
self._parsers += [decl]

def import_module(self, format):
"""Import a module defined in the cache"""
Expand Down
6 changes: 3 additions & 3 deletions conkit/io/tests/test__cache.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,23 +16,23 @@ def test_1(self):

def test_2(self):
c = _ParserCache()
self.assertFalse("casp" in c)
self.assertFalse("foo" in c)

def test_3(self):
c = _ParserCache()
self.assertTrue("casprr" in c.contact_file_parsers)

def test_4(self):
c = _ParserCache()
self.assertFalse("casp" in c.contact_file_parsers)
self.assertFalse("bar" in c.contact_file_parsers)

def test_5(self):
c = _ParserCache()
self.assertTrue("fasta" in c.sequence_file_parsers)

def test_6(self):
c = _ParserCache()
self.assertFalse("fas" in c.sequence_file_parsers)
self.assertFalse("baz" in c.sequence_file_parsers)

def test_7(self):
c = _ParserCache()
Expand Down

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