From f8e443debeac2de829e97f5cdb5acc63aabb2f10 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Tue, 8 Oct 2024 20:41:36 +0200
Subject: [PATCH] Fix type annotations for `LongTargetsPipeline` specific
options and properties
---
pyhmmer/plan7.pyi | 15 +++++++++++----
pyhmmer/plan7.pyx | 36 +++++++++++++++++++-----------------
2 files changed, 30 insertions(+), 21 deletions(-)
diff --git a/pyhmmer/plan7.pyi b/pyhmmer/plan7.pyi
index 8f36d431..2e48f121 100644
--- a/pyhmmer/plan7.pyi
+++ b/pyhmmer/plan7.pyi
@@ -719,10 +719,6 @@ class Pipeline(object):
def bit_cutoffs(self) -> typing.Optional[BIT_CUTOFFS]: ...
@bit_cutoffs.setter
def bit_cutoffs(self, bit_cutoffs: typing.Optional[BIT_CUTOFFS]) -> None: ...
- @property
- def strand(self) -> typing.Optional[STRAND]: ...
- @strand.setter
- def strand(self, strand: typing.Optional[STRAND]) -> None: ...
def arguments(self) -> typing.List[str]: ...
def clear(self) -> None: ...
def search_hmm(
@@ -768,10 +764,13 @@ class LongTargetsPipeline(Pipeline):
alphabet: Alphabet,
background: typing.Optional[Background] = None,
*,
+ strand: typing.Optional[STRAND] = None,
B1: int = 100,
B2: int = 240,
B3: int = 1000,
block_length: int = 1024 * 256,
+ window_length: typing.Optional[int] = None,
+ window_beta: typing.Optional[float] = None,
bias_filter: bool = True,
null2: bool = True,
seed: typing.Optional[int] = None,
@@ -806,6 +805,14 @@ class LongTargetsPipeline(Pipeline):
def strand(self) -> typing.Optional[STRAND]: ...
@strand.setter
def strand(self, strand: typing.Optional[STRAND]) -> None: ...
+ @property
+ def window_beta(self) -> float: ...
+ @window_beta.setter
+ def window_beta(self, window_beta: float) -> None: ...
+ @property
+ def window_length(self) -> typing.Optional[int]: ...
+ @window_length.setter
+ def window_length(self, window_length: typing.Optional[int]) -> None: ...
class Profile(object):
alphabet: Alphabet
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 11c3c647..212f9147 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -487,11 +487,11 @@ cdef class Background:
def __init__(self, Alphabet alphabet, bint uniform=False):
"""__init__(self, alphabet, uniform=False)\n--\n
-
+
Create a new background model for the given ``alphabet``.
Arguments:
- alphabet (`~pyhmmer.easel.Alphabet`): The alphabet to create
+ alphabet (`~pyhmmer.easel.Alphabet`): The alphabet to create
the background model with.
uniform (`bool`): Whether or not to create the null model with
uniform frequencies. Defaults to `False`.
@@ -658,7 +658,7 @@ cdef class Builder:
object window_beta=None,
):
"""__init__(self, alphabet, *, architecture="fast", weighting="pb", effective_number="entropy", prior_scheme="alphabet", symfrac=0.5, fragthres=0.5, wid=0.62, esigma=45.0, eid=0.62, EmL=200, EmN=200, EvL=200, EvN=200, EfL=100, EfN=200, Eft=0.04, seed=42, ere=None, popen=None, pextend=None, score_matrix=None, window_length=None, window_beta=None)\n--\n
-
+
Create a new sequence builder with the given configuration.
Arguments:
@@ -2285,7 +2285,7 @@ cdef class HMM:
def __init__(self, Alphabet alphabet not None, int M, bytes name not None):
"""__init__(self, alphabet, M, name)\n--\n
-
+
Create a new HMM from scratch.
Arguments:
@@ -3051,8 +3051,8 @@ cdef class HMM:
"""Calculate the match occupancy for each match state.
Returns:
- `~pyhmmer.easel.VectorF`: A vector of size :math:`M+1`
- containing the probability that each match state is used
+ `~pyhmmer.easel.VectorF`: A vector of size :math:`M+1`
+ containing the probability that each match state is used
in a sample glocal path through the model.
.. versionadded:: 0.4.10
@@ -3506,7 +3506,7 @@ cdef class HMMFile:
def __init__(self, object file, bint db = True):
"""__init__(self, file, db=True)\n--\n
-
+
Create a new HMM reader from the given file.
Arguments:
@@ -3752,7 +3752,7 @@ cdef class HMMPressedFile:
def __init__(self, object file):
"""__init__(self, file)\n--\n
-
+
Create a new pressed file from the given filename.
Arguments:
@@ -4068,7 +4068,7 @@ cdef class OptimizedProfile:
def __init__(self, int M, Alphabet alphabet):
"""__init__(self, M, alphabet)\n--\n
-
+
Create a new optimized profile from scratch.
Once allocated, you must call the `~OptimizedProfile.convert`
@@ -5060,7 +5060,7 @@ cdef class Pipeline:
str bit_cutoffs=None,
):
"""__init__(self, alphabet, background=None, *, bias_filter=True, null2=True, seed=42, Z=None, domZ=None, F1=0.02, F2=1e-3, F3=1e-5, E=10.0, T=None, domE=10.0, domT=None, incE=0.01, incT=None, incdomE=0.01, incdomT=None, bit_cutoffs=None)\n--\n
-
+
Instantiate and configure a new accelerated comparison pipeline.
Arguments:
@@ -5889,7 +5889,7 @@ cdef class Pipeline:
raise TypeError(f"Expected DigitalSequenceBlock or SequenceFile, found {ty}")
# record query metadata
hits._query = query
- return hits
+ return hits
cpdef TopHits search_seq(
self,
@@ -6534,7 +6534,7 @@ cdef class LongTargetsPipeline(Pipeline):
**kwargs,
):
"""__init__(self, alphabet, background=None, *, F1=0.02, F2=3e-3, F3=3e-5, strand=None, B1=100, B2=240, B3=1000, block_length=0x40000, window_length=None, window_beta=None, **kwargs)\n--\n
-
+
Instantiate and configure a new long targets pipeline.
Arguments:
@@ -6563,6 +6563,8 @@ cdef class LongTargetsPipeline(Pipeline):
target sequences.
window_length (`int`): The window length to use to compute
E-values.
+ window_beta (`float`): The tail mass at which window length
+ is determined.
**kwargs: Any additional parameter will be passed to the
`~pyhmmer.plan7.Pipeline` constructor.
@@ -7068,7 +7070,7 @@ cdef class LongTargetsPipeline(Pipeline):
else:
ty = type(sequences).__name__
raise TypeError(f"Expected DigitalSequenceBlock or SequenceFile, found {ty}")
-
+
hits._query = query
return hits
@@ -7317,7 +7319,7 @@ cdef class Profile:
def __init__(self, int M, Alphabet alphabet):
"""__init__(self, M, alphabet)\n--\n
-
+
Create a new profile for the given ``alphabet``.
Arguments:
@@ -7682,9 +7684,9 @@ cdef class TopHits:
def __init__(self, object query not None):
"""__init__(self, query)\n--\n
-
+
Create an empty `TopHits` instance.
-
+
"""
self._query = query
with nogil:
@@ -8675,7 +8677,7 @@ cdef class Trace:
def __init__(self, posteriors=False):
"""__init__(self, posteriors=False)\n--\n
-
+
Create a new `Trace` object.
Arguments:
--
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