From 21600453d707277b5fbcd4afa4ba0b8c61832824 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Tue, 8 Oct 2024 21:05:04 +0200
Subject: [PATCH] Add `SequenceFile` as an accepted type for most `hmmer`
functions
---
pyhmmer/hmmer.py | 50 +++++++++++++++++++++++-------------------------
1 file changed, 24 insertions(+), 26 deletions(-)
diff --git a/pyhmmer/hmmer.py b/pyhmmer/hmmer.py
index fa1e1fe9..a3835616 100644
--- a/pyhmmer/hmmer.py
+++ b/pyhmmer/hmmer.py
@@ -809,7 +809,7 @@ class _SCANDispatcher(
def hmmsearch(
queries: typing.Union[_P, typing.Iterable[_P]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_P, int], None]] = None,
@@ -884,14 +884,14 @@ def hmmsearch(
queries = (queries,)
if isinstance(sequences, SequenceFile):
- sequence_file: SequenceFile = sequences
- if sequence_file.name is None:
+ # sequence_file = sequences
+ if sequences.name is None:
raise ValueError("expected named `SequenceFile` for targets")
- if not sequence_file.digital:
+ if not sequences.digital:
raise ValueError("expected digital mode `SequenceFile` for targets")
- assert sequence_file.alphabet is not None
- alphabet = alphabet or sequence_file.alphabet
- targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequence_file
+ assert sequences.alphabet is not None
+ alphabet = alphabet or sequences.alphabet
+ targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequences
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -923,7 +923,7 @@ def hmmsearch(
def phmmer(
queries: typing.Union[_M, typing.Iterable[_M]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_M, int], None]] = None,
@@ -1023,7 +1023,7 @@ def phmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1039,7 +1039,7 @@ def jackhmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1055,7 +1055,7 @@ def jackhmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1072,7 +1072,7 @@ def jackhmmer(
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1157,14 +1157,13 @@ def jackhmmer(
queries = (queries,)
if isinstance(sequences, SequenceFile):
- sequence_file: SequenceFile = sequences
- if sequence_file.name is None:
+ if sequences.name is None:
raise ValueError("expected named `SequenceFile` for targets")
- if not sequence_file.digital:
+ if not sequences.digital:
raise ValueError("expected digital mode `SequenceFile` for targets")
- assert sequence_file.alphabet is not None
- alphabet = alphabet or sequence_file.alphabet
- targets = typing.cast(DigitalSequenceBlock, sequence_file.read_block())
+ assert sequences.alphabet is not None
+ alphabet = alphabet or sequences.alphabet
+ targets = typing.cast(DigitalSequenceBlock, sequences.read_block())
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -1206,7 +1205,7 @@ def jackhmmer(
def nhmmer(
queries: typing.Union[_N, typing.Iterable[_N]],
- sequences: typing.Iterable[DigitalSequence],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_N, int], None]] = None,
@@ -1270,14 +1269,13 @@ def nhmmer(
queries = (queries,)
if isinstance(sequences, SequenceFile):
- sequence_file: SequenceFile = sequences
- if sequence_file.name is None:
+ if sequences.name is None:
raise ValueError("expected named `SequenceFile` for targets")
- if not sequence_file.digital:
+ if not sequences.digital:
raise ValueError("expected digital mode `SequenceFile` for targets")
- assert sequence_file.alphabet is not None
- alphabet = alphabet or sequence_file.alphabet
- targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequence_file
+ assert sequences.alphabet is not None
+ alphabet = alphabet or sequences.alphabet
+ targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequences
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -1594,7 +1592,7 @@ if __name__ == "__main__":
with HMMFile(args.hmmfile) as hmms:
if hmms.is_pressed():
hmms = hmms.optimized_profiles() # type: ignore
- hits_list = hmmsearch(hmms, sequences, cpus=args.jobs) # type: ignore
+ hits_list = hmmsearch(hmms, sequences, cpus=args.jobs)
for hits in hits_list:
for hit in hits:
if hit.reported:
--
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