Étienne Mollier pushed to branch upstream at Debian Med / python-pyfaidx
Commits:
4ceb3736 by Étienne Mollier at 2024-08-11T19:14:40+02:00
New upstream version 0.8.1.2
- - - - -
3 changed files:
- − codecov.yml
- pyfaidx/__init__.py
- pyproject.toml
Changes:
=====================================
codecov.yml deleted
=====================================
@@ -1,4 +0,0 @@
-comment: false
-coverage:
- status:
- patch: false
=====================================
pyfaidx/__init__.py
=====================================
@@ -1134,9 +1134,9 @@ class Fasta(object):
return sum(len(record) for record in self)
def get_seq(self, name, start, end, rc=False):
- """Return a sequence by record name and interval [start, end).
+ """Return a sequence by record name and interval [start, end].
- Coordinates are 1-based, end-exclusive.
+ Coordinates are 1-based, closed interval.
If rc is set, reverse complement will be returned.
"""
# Get sequence from real genome object and save result.
@@ -1245,9 +1245,9 @@ class FastaVariant(Fasta):
str(self.gt_type))
def get_seq(self, name, start, end):
- """Return a sequence by record name and interval [start, end).
+ """Return a sequence by record name and interval [start, end].
Replace positions with polymorphism with variant.
- Coordinates are 0-based, end-exclusive.
+ Coordinates are 1-based, closed interval.
"""
seq = self.faidx.fetch(name, start, end)
if self.faidx.as_raw:
=====================================
pyproject.toml
=====================================
@@ -28,7 +28,8 @@ classifiers = [
]
dependencies = [
"setuptools",
- "importlib_metadata"
+ "importlib_metadata",
+ "packaging"
]
dynamic = ["version"]
View it on GitLab:
https://salsa.debian.org/med-team/python-pyfaidx/-/commit/4ceb37365bfcd5955c73649709bf72e7ca4a0120
--
View it on GitLab:
https://salsa.debian.org/med-team/python-pyfaidx/-/commit/4ceb37365bfcd5955c73649709bf72e7ca4a0120
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