From eb94ef9700fa57c85273f9d0a0396a96bf82177e Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 7 Oct 2024 21:02:35 +0200
Subject: [PATCH] Fix recording of query in `TopHits` obtained from a daemon
`Client`
---
pyhmmer/daemon.pyx | 12 +++---------
pyhmmer/plan7.pyx | 31 +++++++++++++++++++------------
2 files changed, 22 insertions(+), 21 deletions(-)
diff --git a/pyhmmer/daemon.pyx b/pyhmmer/daemon.pyx
index db31f05c..d832cf0c 100644
--- a/pyhmmer/daemon.pyx
+++ b/pyhmmer/daemon.pyx
@@ -355,9 +355,7 @@ cdef class Client:
txt = buffer.getvalue()
hits = self._client(txt, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
- hits._qname = query.name
- hits._qacc = query.accession
- hits._qlen = len(query)
+ hits._query = query
return hits
@@ -396,9 +394,7 @@ cdef class Client:
txt = buffer.getvalue()
hits = self._client(txt, db, ranges, pli, p7_pipemodes_e.p7_SEARCH_SEQS)
- hits._qname = query.name
- hits._qacc = query.accession
- hits._qlen = query.M
+ hits._query = query
return hits
@@ -430,9 +426,7 @@ cdef class Client:
txt = buffer.getvalue()
hits = self._client(txt, db, None, pli, p7_pipemodes_e.p7_SCAN_MODELS)
- hits._qname = query.name
- hits._qacc = query.accession
- hits._qlen = len(query)
+ hits._query = query
return hits
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 743866e4..9b5fc58c 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -7749,7 +7749,7 @@ cdef class TopHits:
hits.append(offset)
return {
- "query": self.query,
+ "query": self._query,
"unsrt": unsrt,
"hit": hits,
"Nalloc": self._th.Nalloc,
@@ -7815,7 +7815,7 @@ cdef class TopHits:
cdef VectorU8 hit_state
# record query name and accession
- self.query = state["query"]
+ self._query = state["query"]
# deallocate current data if needed
if self._th != NULL:
@@ -7924,6 +7924,8 @@ cdef class TopHits:
.. versionadded:: 0.6.1
"""
+ if self._query is None:
+ return None
return self._query.name
@property
@@ -7933,6 +7935,8 @@ cdef class TopHits:
.. versionadded:: 0.6.1
"""
+ if self._query is None:
+ return None
return self._query.accession
@property
@@ -7942,6 +7946,8 @@ cdef class TopHits:
.. versionadded:: 0.10.5
"""
+ if self._query is None:
+ return 0
return self._query.M if isinstance(self._query, HMM) else len(self._query)
@property
@@ -8214,9 +8220,7 @@ cdef class TopHits:
cdef TopHits copy = TopHits.__new__(TopHits)
# record query metatada
- copy._qname = self._qname
- copy._qacc = self._qacc
- copy._qlen = self._qlen
+ copy._query = self._query
with nogil:
# copy pipeline configuration
@@ -8442,9 +8446,14 @@ cdef class TopHits:
cdef FILE* file
cdef str fname
cdef int status
- cdef char* unk = b"-"
- cdef char* qname = unk if self._qname is None else <char*> self._qname
- cdef char* qacc = unk if self._qacc is None else <char*> self._qacc
+ cdef bytes qname = b"-"
+ cdef bytes qacc = b"-"
+
+ if self._query is not None:
+ if self._query.name is not None:
+ qname = self._query.name
+ if self._query.accession is not None:
+ qacc = self._query.accession
file = fopen_obj(fh, "w")
try:
@@ -8536,10 +8545,8 @@ cdef class TopHits:
other_copy = other.copy()
# just store the copy if merging inside an empty uninitialized `TopHits`
- if merged._th.N == 0 and merged._qname is None and merged._qacc is None:
- merged._qname = other._qname
- merged._qacc = other._qacc
- merged._qlen = other._qlen
+ if merged._th.N == 0 and merged._query is None:
+ merged._query = other._query
memcpy(&merged._pli, &other_copy._pli, sizeof(P7_PIPELINE))
merged._th, other_copy._th = other_copy._th, merged._th
continue
--
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