From 4fa36ad15d9f6f1d9aa30570e90c7fab9633fb64 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 15 Nov 2021 18:13:22 +0100
Subject: [PATCH] Add property to access the index of a `Mapper` minimizer
positions
---
pyfastani/_fastani.pyi | 28 +++++-
pyfastani/_fastani.pyx | 215 ++++++++++++++++++++++++++++++++++++-----
2 files changed, 216 insertions(+), 27 deletions(-)
diff --git a/pyfastani/_fastani.pyi b/pyfastani/_fastani.pyi
index 1014713..529973d 100644
--- a/pyfastani/_fastani.pyi
+++ b/pyfastani/_fastani.pyi
@@ -1,5 +1,5 @@
import typing
-from typing import Dict, Generic, List, Union, Iterable, Tuple, TypeVar
+from typing import Any, Dict, Generic, List, Union, Iterable, Tuple, TypeVar
N = TypeVar("N")
Seq = Union[str, bytes, bytearray, memoryview]
@@ -22,6 +22,7 @@ class _Parameterized:
@property
def protein(self) -> bool: ...
+
class Sketch(Generic[N], _Parameterized):
def __init__(
self,
@@ -60,8 +61,7 @@ class Hit(Generic[N]):
def __init__(self, name: N, identity: float, matches: int, fragments: int): ...
def __repr__(self) -> str: ...
def __eq__(self, other: object) -> bool: ...
- def __getstate__(self) -> Tuple[N, float, int, int]: ...
- def __setstate__(self, state: Tuple[N, float, int, int]) -> None: ...
+ def __reduce__(self) -> Tuple[Any, ...]: ...
@property
def name(self) -> N: ...
@property
@@ -84,3 +84,25 @@ class MinimizerInfo:
def sequence_id(self) -> int: ...
@property
def window_position(self) -> int: ...
+
+
+class Position:
+ def __init__(self, sequence_id: int, window_position: int): ...
+ def __repr__(self) -> str: ...
+ def __eq__(self, other: object) -> bool: ...
+ def __reduce__(self) -> Tuple[Any, ...]: ...
+ @property
+ def sequence_id(self) -> int: ...
+ @property
+ def window_position(self) -> int: ...
+
+
+class MinimizerIndex(typing.MutableMapping[int, List[Position]]):
+ def __init__(self) -> None: ...
+ def __len__(self) -> int: ...
+ def __iter__(self) -> typing.Iterator[int]: ...
+ def __contains__(self, item: object) -> bool: ...
+ def __getitem__(self, item: int) -> List[Position]: ...
+ def __setitem__(self, item: int, value: List[Position]) -> None: ...
+ def __delitem__(self, item: int) -> None: ...
+ def __reduce__(self) -> Tuple[Any, ...]: ...
diff --git a/pyfastani/_fastani.pyx b/pyfastani/_fastani.pyx
index 975406e..2354e64 100644
--- a/pyfastani/_fastani.pyx
+++ b/pyfastani/_fastani.pyx
@@ -746,13 +746,7 @@ cdef class Mapper(_Parameterized):
"sequencesByFileInfo": list(self._sk.sequencesByFileInfo),
"minimizerIndex": self.minimizers,
"minimizerFreqHistogram": dict(self._sk.minimizerFreqHistogram),
- "minimizerPosLookupIndex": {
- pair.first:[
- (minimizer.seqId, minimizer.wpos)
- for minimizer in pair.second
- ]
- for pair in self._sk.minimizerPosLookupIndex
- },
+ "minimizerPosLookupIndex": self.lookup_index,
}
}
@@ -768,17 +762,15 @@ cdef class Mapper(_Parameterized):
for minimizer in state["sketch"]["minimizerIndex"]:
self._sk.minimizerIndex.push_back(minimizer.to_raw())
- cdef seqno_t seqId
+ cdef seqno_t seqId
cdef offset_t wpos
- cdef MinimizerMetaData_t mini
+ cdef Position pos
cdef vector[MinimizerMetaData_t] map_value
self._sk.minimizerPosLookupIndex = unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t]()
for key, value in state["sketch"]["minimizerPosLookupIndex"].items():
map_value = vector[MinimizerMetaData_t]()
- for (seqId, wpos) in value:
- mini.seqId = seqId
- mini.wpos = wpos
- map_value.push_back(mini)
+ for pos in value:
+ map_value.push_back(pos.to_raw())
self._sk.minimizerPosLookupIndex.insert(pair[MinimizerMapKeyType_t, MinimizerMapValueType_t](key, map_value))
# --- Properties ---------------------------------------------------------
@@ -803,6 +795,20 @@ cdef class Mapper(_Parameterized):
return minis
+ @property
+ def lookup_index(self):
+ """`MinimizerLookupIndex`: The index of initial minimizer positions.
+
+ This table is used to retrieve at which positions the minimizers
+ appear in the reference genomes.
+
+ """
+ assert self._sk != nullptr
+ cdef MinimizerIndex index = MinimizerIndex.__new__(MinimizerIndex)
+ index._map = &self._sk.minimizerPosLookupIndex
+ index.owner = self
+ return index
+
# --- Methods ------------------------------------------------------------
@staticmethod
@@ -1124,7 +1130,7 @@ cdef class Hit:
def __repr__(self):
cdef str ty = type(self).__name__
- return "{}(name={!r}, identity={!r} matches={!r}, fragments={!r})".format(
+ return "{}(name={!r}, identity={!r}, matches={!r}, fragments={!r})".format(
ty, self.name, self.identity, self.matches, self.fragments
)
@@ -1136,11 +1142,11 @@ cdef class Hit:
and self.identity == other.identity
)
- def __getstate__(self):
- return self.name, self.matches, self.fragments, self.identity
-
- def __setstate__(self, state):
- self.name, self.matches, self.fragments, self.identity = state
+ def __reduce__(self):
+ return (
+ Hit,
+ (self.name, self.identity, self.matches, self.fragments)
+ )
cdef class MinimizerInfo:
@@ -1178,11 +1184,11 @@ cdef class MinimizerInfo:
and self.window_position == other.window_position
)
- def __getstate__(self):
- return self.hash, self.sequence_id, self.window_position
-
- def __setstate__(self, state):
- self.hash, self.sequence_id, self.window_position = state
+ def __reduce__(self):
+ return (
+ MinimizerInfo,
+ (self.hash, self.sequence_id, self.window_position)
+ )
# --- Methods ------------------------------------------------------------
@@ -1196,3 +1202,164 @@ cdef class MinimizerInfo:
info.seqId = self.sequence_id
info.wpos = self.window_position
return info
+
+
+cdef class Position:
+
+ # --- Attributes ---------------------------------------------------------
+
+ cdef readonly seqno_t sequence_id
+ cdef readonly offset_t window_position
+
+ # --- Magic methods ------------------------------------------------------
+
+ def __init__(self, seqno_t sequence_id, offset_t window_position):
+ """__init__(self, sequence_id, window_position)\n--
+
+ Create a new `Position` instance with the given parameters.
+
+ """
+ self.sequence_id = sequence_id
+ self.window_position = window_position
+
+ def __repr__(self):
+ cdef str ty = type(self).__name__
+ return "{}(sequence_id={!r}, window_position={!r})".format(
+ ty, self.sequence_id, self.window_position
+ )
+
+ def __eq__(self, Position other):
+ return (
+ self.sequence_id == other.sequence_id
+ and self.window_position == other.window_position
+ )
+
+ def __reduce__(self):
+ return (
+ Position,
+ (self.sequence_id, self.window_position)
+ )
+
+ # --- Methods ------------------------------------------------------------
+
+ @staticmethod
+ cdef Position from_raw(MinimizerMetaData_t raw):
+ return Position(raw.seqId, raw.wpos)
+
+ cdef MinimizerMetaData_t to_raw(self):
+ cdef MinimizerMetaData_t m
+ m.seqId = self.sequence_id
+ m.wpos = self.window_position
+ return m
+
+
+cdef class MinimizerIndex:
+ """The index mapping minimizer hash values to their positions.
+ """
+
+ # --- Attributes ---------------------------------------------------------
+
+ cdef Sketch_t.MI_Map_t* _map
+ cdef object owner
+
+ # --- Magic methods ------------------------------------------------------
+
+ def __cinit__(self):
+ # create a new Sketch with the parameters
+ self._map = NULL
+ self.owner = None
+
+ def __init__(self):
+ self._map = new Sketch_t.MI_Map_t()
+
+ def __dealloc__(self):
+ if self.owner is None:
+ del self._map
+
+ def __len__(self):
+ assert self._map != NULL
+ return self._map.size()
+
+ def __iter__(self):
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].iterator it
+ it = self._map.begin()
+ while it != self._map.end():
+ yield dereference(it).first
+ preincrement(it)
+
+ def __contains__(self, hash_t item):
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].const_iterator find_it
+ find_it = self._map.const_find(item)
+ return find_it != self._map.end()
+
+ def __getitem__(self, hash_t item):
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].iterator find_it
+ find_it = self._map.find(item)
+ if find_it != self._map.end():
+ return [Position.from_raw(x) for x in dereference(find_it).second]
+ raise KeyError(item)
+
+ def __setitem__(self, hash_t item, object value):
+ # convert value to vector
+ cdef Position position
+ cdef MinimizerMapValueType_t positions = MinimizerMapValueType_t()
+ for position in value:
+ positions.push_back(position.to_raw())
+ # remove previous element if any
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].iterator find_it
+ find_it = self._map.find(item)
+ if find_it != self._map.end():
+ self._map.erase(find_it)
+ # add new element
+ cdef pair[MinimizerMapKeyType_t, MinimizerMapValueType_t] element
+ element.first = item
+ element.second = positions
+ self._map.insert(element)
+
+ def __delitem__(self, hash_t item):
+ # remove previous element if any
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].iterator find_it
+ find_it = self._map.find(item)
+ if find_it != self._map.end():
+ self._map.erase(find_it)
+ else:
+ raise KeyError(item)
+
+ def __reduce__(self):
+ return (
+ MinimizerIndex,
+ (),
+ None,
+ None,
+ self.items(),
+ None
+ )
+
+ # --- Methods ------------------------------------------------------------
+
+ def items(self):
+ cdef MinimizerMetaData_t pos_raw
+ cdef MinimizerMapKeyType_t key
+ cdef MinimizerMapValueType_t value
+ cdef size_t i
+ cdef list positions
+ cdef Position position
+ cdef unordered_map[MinimizerMapKeyType_t, MinimizerMapValueType_t].iterator it
+
+ it = self._map.begin()
+ while it != self._map.end():
+
+ key = dereference(it).first
+ value = dereference(it).second
+
+ i = 0
+ positions = PyList_New(value.size())
+
+ for pos_raw in value:
+ pos = Position.from_raw(pos_raw)
+ Py_INCREF(pos)
+ PyList_SET_ITEM(positions, i, pos)
+ i += 1
+
+ yield key, positions
+ preincrement(it)
--
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