pyaragorn 0.1.0__pp39-pypy39_pp73-win_amd64.whl → 0.2.0__pp39-pypy39_pp73-win_amd64.whl

pyaragorn/lib.pyi

@@ -0,0 +1,89 @@
+import typing
+from typing import Literal, Union, Generic
+from typing_extensions import Buffer
+
+__version__: str
+
+ARAGORN_VERSION: str
+TRANSLATION_TABLES: typing.Set[int]
+
+class Gene:
+    @property
+    def type(self) -> str: ...
+    @property
+    def begin(self) -> int: ...
+    @property
+    def end(self) -> int: ...
+    @property
+    def length(self) -> int: ...
+    @property
+    def strand(self) -> Literal[1, -1]: ...
+    @property
+    def energy(self) -> float: ...
+    def sequence(self) -> str: ...
+ 
+class TRNAGene(Gene):
+    @property
+    def type(self) -> Literal["tRNA"]: ...
+    @property
+    def amino_acid(self) -> str: ...
+    @property
+    def amino_acids(self) -> Union[Tuple[str], Tuple[str, str]]: ...
+    @property
+    def anticodon(self) -> str: ...
+    @property
+    def anticodon_offset(self) -> int: ...
+    @property
+    def anticodon_length(self) -> Literal[2, 3, 4]: ...
+
+class TMRNAGene(Gene):
+    @property
+    def type(self) -> Literal["tmRNA"]: ...
+    @property
+    def permuted(self) -> bool: ...
+    @property
+    def orf_offset(self) -> int: ...
+    @property
+    def orf_length(self) -> int: ...
+    def orf(self, include_stop: bool = True) -> str: ...
+    def peptide(self, include_stop: bool = True) -> str: ...
+
+
+class Cursor:
+    def __init__(self, obj: Union[str, bytes, bytearray, Buffer]) -> None: ...
+
+
+G = typing.TypeVar("G", bound=Gene)
+
+class RNAFinder(Generic[G]):
+    @typing.overload
+    def __init__(
+        self: RNAFinder[TRNAGene],
+        translation_table: int = 1,
+        *,
+        tmrna: Literal[False],
+        trna: Literal[True] = True,
+        linear: bool = False,
+    ) -> None: ...
+    @typing.overload
+    def __init__(
+        self: RNAFinder[TMRNAGene],
+        translation_table: int = 1,
+        *,
+        trna: Literal[False],
+        tmrna: Literal[True] = True,
+        linear: bool = False,
+    ) -> None: ...
+    @typing.overload
+    def __init__(
+        self: RNAFinder[Union[TRNAGene, TMRNAGene]],
+        translation_table: int = 1,
+        *,
+        trna: bool = True,
+        tmrna: bool = True,
+        linear: bool = False,
+    ) -> None: ...
+    def find_rna(
+        self,
+        sequence: Union[str, bytes, bytearray, Buffer],
+    ) -> List[G]: ...

pyaragorn/lib.pyx

@@ -204,12 +204,29 @@ cdef class TRNAGene(Gene):
 
     @property
     def amino_acid(self):
-        """`str` or (`str`, `str`): The 3-letter amino-acid(s) for this gene.
+        """`str`: The 3-letter amino-acid(s) for this gene.
 
         Hint:
-            A single string is given if the anticodon loop was identified
-            with exactly 3 nucleotides. Otherwise, this property stores
-            a pair of amino-acids.
+            If the anticodon loop contains 6 or 8 bases, ``???`` is
+            returned.
+
+        """
+        cdef csw sw
+        cdef int* s = self._gene.seq + self._gene.anticodon
+        (<int*> &sw.geneticcode)[0] = self._genetic_code
+        if self._gene.cloop == 6 or self._gene.cloop == 8:
+            return "???"
+        else:
+            return aragorn.aa(s, &sw).decode('ascii')
+
+    @property
+    def amino_acids(self):
+        """`tuple` of `str`: All possible 3-letter amino-acids for this gene.
+
+        Hint:
+            If the anticodon loop contains 6 or 8 bases, a tuple of two
+            amino-acid is returned, otherwise a tuple with a single element
+            is returned.
 
         """
         cdef csw sw
@@ -277,14 +294,20 @@ cdef class TMRNAGene(Gene):
     """
 
     @property
-    def cds_offset(self):
-        """`int`: The offset in the gene at which the coding sequence starts.
+    def permuted(self):
+        """`bool`: Whether this tmRNA gene is a permuted gene.
+        """
+        return self._gene.asst != 0
+
+    @property
+    def orf_offset(self):
+        """`int`: The offset in the gene at which the open-reading frame starts.
         """
         return self._gene.tps + 1
 
     @property
-    def cds_length(self):
-        """`int`: The length of the coding sequence (in nucleotides).
+    def orf_length(self):
+        """`int`: The length of the open-reading frame (in nucleotides).
         """
         cdef int  tpe    = self._gene.tpe
         cdef int* se     = (self._gene.eseq + tpe) + 1
@@ -300,8 +323,8 @@ cdef class TMRNAGene(Gene):
 
         return tpe - self._gene.tps
 
-    def cds(self, include_stop=True):
-        """Retrieve the coding sequence of the mRNA-like region.
+    def orf(self, include_stop=True):
+        """Retrieve the open-reading frame of the mRNA-like region.
 
         Arguments:
             include_stop (`bool`): Whether or not to include the STOP codons
@@ -481,7 +504,7 @@ cdef class RNAFinder:
 
         Returns:
             `list` of `~pyaragorn.Gene`: A list of `~pyaragorn.Gene` (either
-            `~pyaragorn.TRNAGene` or `~pyaragorn.TMRNAGene`) corresponding 
+            `~pyaragorn.TRNAGene` or `~pyaragorn.TMRNAGene`) corresponding
             to RNA genes detected in the sequence according to the `RNAFinder`
             parameters.
 

pyaragorn/tests/test_rna_finder.py

@@ -46,11 +46,11 @@ class TestRNAFinder(unittest.TestCase):
                 self.assertEqual(gene.sequence().lower(), seq)
             elif gene.type == "tmRNA":
                 matched = _TMRNA_RX.match(result)
-                _, complement, begin, end, energy, cds_start, cds_end, peptide = matched.groups()
+                _, complement, begin, end, energy, orf_start, orf_end, peptide = matched.groups()
                 self.assertEqual(gene.begin, int(begin))
                 self.assertEqual(gene.end, int(end))
-                self.assertEqual(gene.cds_offset, int(cds_start))
-                self.assertEqual(gene.cds_offset + gene.cds_length, int(cds_end))
+                self.assertEqual(gene.orf_offset, int(orf_start))
+                self.assertEqual(gene.orf_offset + gene.orf_length, int(orf_end))
                 self.assertEqual(gene.peptide(), peptide)
                 self.assertEqual(gene.strand, -1 if complement == "c" else +1)
                 self.assertAlmostEqual(gene.energy, float(energy), places=1)
@@ -66,4 +66,4 @@ class TestRNAFinder(unittest.TestCase):
         record = data.load_record("CP001621.fna.gz")
         finder = RNAFinder(translation_table=11, tmrna=True, trna=False)
         for gene in finder.find_rna(str(record.seq)):
-            self.assertIsInstance(gene, TMRNAGene)
+            self.assertIsInstance(gene, TMRNAGene)

{pyaragorn-0.1.0.dist-info → pyaragorn-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyaragorn
-Version: 0.1.0
+Version: 0.2.0
 Summary: Cython bindings and Python interface to ARAGORN, a tRNA and mtRNA detection software.
 Keywords: bioinformatics,gene,transfer,messenger,RNA
 Author-Email: Martin Larralde <martin.larralde@embl.de>
@@ -697,6 +697,7 @@ Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
 Project-URL: Documentation, https://pyaragorn.readthedocs.io/en/stable/
 Project-URL: Bug Tracker, https://github.com/althonos/pyaragorn/issues
 Project-URL: Changelog, https://github.com/althonos/pyaragorn/blob/master/CHANGELOG.md

{pyaragorn-0.1.0.dist-info → pyaragorn-0.2.0.dist-info}/RECORD

@@ -1,7 +1,9 @@
 pyaragorn/__init__.py,sha256=yk11uoNKEEy1QI8XtudgwKJh7mAUdC-SH6RXUh0-x3A,872
 pyaragorn/CMakeLists.txt,sha256=Kv6Kqg594zByfDsm_usgax9nTlF6PtciSTtUcUe2QHs,35
-pyaragorn/lib.pypy39-pp73-win_amd64.pyd,sha256=F50-SdYfc5j4uw9rWKKO_lrQYJROYhdDGIa1wi02xKg,462848
-pyaragorn/lib.pyx,sha256=-J2T0SXAz_2hNVSg5QUt5JxC1-52iSSEoYuzVn0bFy4,24060
+pyaragorn/lib.pyi,sha256=ylr2aKYkmrA3emLY6EVdn2fLmTogKbOkkgRUY3WHHpc,2331
+pyaragorn/lib.pypy39-pp73-win_amd64.pyd,sha256=SCDRJCDnjfaKR7AiHQQVBQeqAw6VCFbY4lMeOa1aaiI,463872
+pyaragorn/lib.pyx,sha256=dO5cTTcBhFEffDQhg3Nw5QeRnyaW8vGvgAvo86RsJwA,24742
+pyaragorn/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyaragorn/tests/__init__.py,sha256=A_IoY00uMA3HQ7Qjorm5Pr2Tg7n3J2lnCzJyiCAW4lY,242
 pyaragorn/tests/data/__init__.py,sha256=JnSWGIo3ThkKlbZLTFxP-fVBxSTN4Yw5YAzQqa_IpXM,705
 pyaragorn/tests/data/CP001621.default.txt,sha256=40AQzlXhPr9mXrryFw0Nc67REf3MLZ2BNHG-7CRQvAU,6874
@@ -9,8 +11,8 @@ pyaragorn/tests/data/CP001621.fna.gz,sha256=dSAI3T64jSevuR4p0JXBNaTmMlCRsbbY6bCC
 pyaragorn/tests/fasta.py,sha256=Ocgd_9WusRLFVBxt9ZViNNhT9yr8S5-BlVJi5GkSUuQ,2826
 pyaragorn/tests/requirements.txt,sha256=uy1xEQvsQwXz38J-DhiHWzGmgxiJMlbNuz_M2jvifDI,46
 pyaragorn/tests/test_doctest.py,sha256=TMtD6iAGDRbaRJFSsTlLAxm-FR02FAfVFFCsOR_7hao,3235
-pyaragorn/tests/test_rna_finder.py,sha256=9lLCfAv9FmxFTC06Wb7RP-2h-1TP_utxm2oqUINNu5Y,3283
-pyaragorn-0.1.0.dist-info/METADATA,sha256=wbtQTwEEy23vYJQEVezQIaEB6Z405rxwf-cDW8DGzpg,51735
-pyaragorn-0.1.0.dist-info/WHEEL,sha256=kmyLEt6PTDdepfBWae_IEheSXQSU1loiwfrmHYbmDtI,111
-pyaragorn-0.1.0.dist-info/licenses/COPYING,sha256=lE9DJUN_D0B-V6xgf_SX0xjldzX1TGs1xKyMvBdnWCM,35822
-pyaragorn-0.1.0.dist-info/RECORD,,
+pyaragorn/tests/test_rna_finder.py,sha256=SnEJw_4mc1Nv2RvT34PIcMeN-qDRQRw2IraChy-HEZ0,3285
+pyaragorn-0.2.0.dist-info/METADATA,sha256=TpQ3g48XDRhyyQl37Cs6_IQ2AIyJB9bEMOLuvq5RIT4,51763
+pyaragorn-0.2.0.dist-info/WHEEL,sha256=F_HDvWacHASfq-j7PPZd4zU82nzVm_VIZzDXcalXAG0,111
+pyaragorn-0.2.0.dist-info/licenses/COPYING,sha256=lE9DJUN_D0B-V6xgf_SX0xjldzX1TGs1xKyMvBdnWCM,35822
+pyaragorn-0.2.0.dist-info/RECORD,,

{pyaragorn-0.1.0.dist-info → pyaragorn-0.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.3
+Generator: scikit-build-core 0.11.4
 Root-Is-Purelib: false
 Tag: pp39-pypy39_pp73-win_amd64