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Martin Larralde
pyrodigal
Commits
069d11cf
Commit
069d11cf
authored
Apr 06, 2022
by
Martin Larralde
Browse files
Add `Gene.score` property to get a gene score as reported in the score data
parent
1f1528ee
Changes
2
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Inline
Side-by-side
pyrodigal/_pyrodigal.pyi
View file @
069d11cf
...
...
@@ -162,6 +162,8 @@ class Gene:
def tscore(self) -> float: ...
@property
def uscore(self) -> float: ...
@property
def score(self) -> float: ...
def confidence(self) -> float: ...
def sequence(self) -> str: ...
def translate(self, translation_table: Optional[int] = None, unknown_residue: str = "X") -> str: ...
...
...
pyrodigal/_pyrodigal.pyx
View file @
069d11cf
...
...
@@ -2380,7 +2380,7 @@ cdef class Gene:
def
_score_data
(
self
):
return
"conf={:.2f};score={:.2f};cscore={:.2f};sscore={:.2f};rscore={:.2f};uscore={:.2f};tscore={:.2f}"
.
format
(
self
.
confidence
(),
self
.
cscore
+
self
.
s
score
,
self
.
score
,
self
.
cscore
,
self
.
sscore
,
self
.
rscore
,
...
...
@@ -2554,6 +2554,16 @@ cdef class Gene:
"""
return
self
.
owner
.
nodes
.
nodes
[
self
.
gene
.
start_ndx
].
uscore
@
property
def
score
(
self
):
"""`float`: The gene score, sum of the coding and start codon scores.
.. versionadded:: 0.7.3
"""
cdef
_node
*
node
=
&
self
.
owner
.
nodes
.
nodes
[
self
.
gene
.
start_ndx
]
return
node
.
cscore
+
node
.
sscore
@
property
def
start_node
(
self
):
"""`~pyrodigal.Node`: The start node at the beginning of this gene.
...
...
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