From 41c377e648babcb511ae1f6baf16c98496564f5a Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Tue, 8 Oct 2024 15:25:34 +0200
Subject: [PATCH] Fix handling of `TopHits` in `pyhmmer.daemon.Client`
---
pyhmmer/daemon.pxd | 2 +-
pyhmmer/daemon.pyx | 51 +++++++++++-----------------------------------
2 files changed, 13 insertions(+), 40 deletions(-)
diff --git a/pyhmmer/daemon.pxd b/pyhmmer/daemon.pxd
index 199c6159..4aa1f2cd 100644
--- a/pyhmmer/daemon.pxd
+++ b/pyhmmer/daemon.pxd
@@ -22,7 +22,7 @@ cdef class Client:
cdef bytearray _recvall(self, size_t message_size)
cdef TopHits _client(
self,
- bytes query,
+ object query,
uint64_t db,
list ranges,
Pipeline pli,
diff --git a/pyhmmer/daemon.pyx b/pyhmmer/daemon.pyx
index d832cf0c..c161e5ca 100644
--- a/pyhmmer/daemon.pyx
+++ b/pyhmmer/daemon.pyx
@@ -160,7 +160,7 @@ cdef class Client:
cdef TopHits _client(
self,
- bytes query,
+ object query,
uint64_t db,
list ranges,
Pipeline pli,
@@ -190,7 +190,7 @@ cdef class Client:
cdef uint32_t hits_start
cdef uint32_t buf_offset = 0
- cdef TopHits hits = TopHits()
+ cdef TopHits hits = TopHits(query)
cdef str options = "".join(pli.arguments())
# check ranges argument
@@ -207,6 +207,12 @@ cdef class Client:
memset(&search_status, 0, sizeof(HMMD_SEARCH_STATUS))
search_stats.hit_offsets = NULL
+ # serialize query
+ with io.BytesIO() as buffer:
+ query.write(buffer)
+ buffer.write(b"\n//")
+ txt = buffer.getvalue()
+
try:
# send the options
if mode == p7_pipemodes_e.p7_SEARCH_SEQS:
@@ -220,7 +226,7 @@ cdef class Client:
self.socket.sendall(f"@--hmmdb {db} {options}\n".encode("ascii"))
# send the query
- self.socket.sendall(query)
+ self.socket.sendall(txt)
# get the search status back
response = self._recvall(HMMD_SEARCH_STATUS_SERIAL_SIZE)
@@ -344,20 +350,9 @@ cdef class Client:
sequence against the sequence database loaded on the server side.
"""
- cdef bytes txt
- cdef TopHits hits
cdef Alphabet abc = getattr(query, "alphabet", Alphabet.amino())
cdef Pipeline pli = Pipeline(abc, **options)
-
- with io.BytesIO() as buffer:
- query.write(buffer)
- buffer.write(b"\n//")
- txt = buffer.getvalue()
-
- hits = self._client(txt, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
- hits._query = query
-
- return hits
+ return self._client(query, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
def search_hmm(
self,
@@ -384,19 +379,8 @@ cdef class Client:
server side.
"""
- cdef bytes txt
- cdef TopHits hits
cdef Pipeline pli = Pipeline(query.alphabet, **options)
-
- with io.BytesIO() as buffer:
- query.write(buffer)
- buffer.write(b"\n//")
- txt = buffer.getvalue()
-
- hits = self._client(txt, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
- hits._query = query
-
- return hits
+ return self._client(query, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
def scan_seq(self, Sequence query, uint64_t db = 1, **options):
"""Search the HMMER daemon database with a query sequence.
@@ -415,20 +399,9 @@ cdef class Client:
server side.
"""
- cdef bytes txt
- cdef TopHits hits
cdef Alphabet abc = getattr(query, "alphabet", Alphabet.amino())
cdef Pipeline pli = Pipeline(abc, **options)
-
- with io.BytesIO() as buffer:
- query.write(buffer)
- buffer.write(b"\n//")
- txt = buffer.getvalue()
-
- hits = self._client(txt, db, None, pli, p7_pipemodes_e.p7_SCAN_MODELS)
- hits._query = query
-
- return hits
+ return self._client(query, db, None, pli, p7_pipemodes_e.p7_SCAN_MODELS)
def iterate_seq(
self,
--
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