From 8b41a59a7d451dbaf23124b3992477a2d7d244a7 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Thu, 6 Jun 2024 15:09:39 +0200
Subject: [PATCH] Make `HMMFile` and `HMMPressedFile` raise `AlphabetMismatch`
on files with mixed alphabets
---
pyhmmer/easel.pyx | 2 +-
pyhmmer/plan7.pyx | 13 +++++++++----
2 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/pyhmmer/easel.pyx b/pyhmmer/easel.pyx
index ee243d4f..5f87047a 100644
--- a/pyhmmer/easel.pyx
+++ b/pyhmmer/easel.pyx
@@ -3716,7 +3716,7 @@ cdef class TextMSA(MSA):
return new
elif status == libeasel.eslEINVAL:
err_msg = errbuf.decode("utf-8", "replace")
- raise ValueError(f"Cannot digitize MSA with alphabet {alphabet}: {err_msg}")
+ raise ValueError(f"Cannot digitize MSA with {alphabet.type} alphabet: {err_msg}")
else:
raise UnexpectedError(status, "esl_msa_Digitize")
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index b5cf9316..6f8b873e 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -3610,6 +3610,9 @@ cdef class HMMFile:
file, or when the file could not be parsed.
`~pyhmmer.errors.AllocationError`: When memory for the HMM could
not be allocated successfully.
+ `~pyhmmer.errors.AlphabetMismatch`: When the file contains HMMs
+ in different alphabets, or in an alphabet that is different
+ from the alphabet used to initialize the `HMMFile`.
.. versionadded:: 0.4.11
@@ -3638,8 +3641,7 @@ cdef class HMMFile:
elif status == libeasel.eslEFORMAT:
raise ValueError("Invalid format in file: {}".format(self._hfp.errbuf.decode("utf-8", "replace")))
elif status == libeasel.eslEINCOMPAT:
- alphabet = libeasel.alphabet.esl_abc_DecodeType(self._alphabet.type)
- raise ValueError("HMM is not in the expected {} alphabet".format(alphabet))
+ raise AlphabetMismatch(self._alphabet)
else:
_reraise_error()
raise UnexpectedError(status, "p7_hmmfile_Read")
@@ -3818,6 +3820,10 @@ cdef class HMMPressedFile:
closed file, or when the file could not be parsed.
`~pyhmmer.errors.AllocationError`: When memory for the
`OptimizedProfile` could not be allocated successfully.
+ `~pyhmmer.errors.AlphabetMismatch`: When the file contains
+ optimized profiles in different alphabets, or in an alphabet
+ that is different from the alphabet used to initialize the
+ `HMMFile`.
.. versionadded:: 0.4.11
@@ -3845,8 +3851,7 @@ cdef class HMMPressedFile:
elif status == libeasel.eslEFORMAT:
raise ValueError("Invalid format in file: {}".format(self._hfp.errbuf.decode("utf-8", "replace")))
elif status == libeasel.eslEINCOMPAT:
- alphabet = libeasel.alphabet.esl_abc_DecodeType(self._alphabet.type)
- raise ValueError("HMM is not in the expected {} alphabet".format(alphabet))
+ raise AlphabetMismatch(self._alphabet)
else:
_reraise_error()
raise UnexpectedError(status, "p7_oprofile_ReadMSV")
--
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