MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

Commit 2525d92a authored by htyao's avatar htyao
Browse files

Update

parent 44e11944
::: varnaapi.VARNA
......@@ -2,7 +2,12 @@
site_name: VARNA API
theme:
name: "material"
name: "readthedocs"
# name: "material"
nav:
- Overview: index.md
- API: varnaapi.md
plugins:
- search
......
......@@ -73,14 +73,16 @@ def assert_valid_interval(length, *args):
def check_structure(ss):
pass
def bp_to_struct(bps):
def _bp_to_struct(bps):
"""Base pair list to structure"""
n = max([j for i, j in bps]) + 1
ss = [-1 for i in range(n)]
for i, j in bps:
ss[i], ss[j] = j, i
return ss
def parse_vienna(ss):
def _parse_vienna(ss):
"""
Parse secondary structure in dot-bracket notation
"""
......@@ -119,12 +121,12 @@ class VARNA:
if len(first)==1:
self.structure = check_structure(structure)
elif len(first)==2:
self.structure = bp_to_struct(structure)
self.structure = _bp_to_struct(structure)
else:
raise Exception("Unrecognized structure format for %s"%(structure))
# Dot-Bracket Notation
elif isinstance(structure, str):
self.structure = parse_vienna(structure)
self.structure = _parse_vienna(structure)
self.dbn = structure
self.length = len(self.structure)
if seq is not None:
......
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