Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: change the encoding into utf-8 #8

Merged
merged 5 commits into from
Sep 15, 2023
Merged

fix: change the encoding into utf-8 #8

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
aa922ea
fix: change the encoding into utf-8
MistyField Jul 27, 2023
5b1aa28
fix: fix bugs on get references of a reaction
MistyField Jul 29, 2023
0a316c5
feat: update branch with master branch
MistyField Sep 14, 2023
f876437
feat: add .idea in .gitignore
MistyField Sep 14, 2023
4e09fa0
fix: remove .idea in .gitignore
MistyField Sep 15, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 3 additions & 4 deletions src/brendapyrser/parser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,8 @@ class BRENDA:
"""
Provides methods to parse the BRENDA database (https://www.brenda-enzymes.org/)
"""

def __init__(self, path_to_database):
with open(path_to_database, encoding="iso-8859-1") as file:
with open(path_to_database, encoding="utf-8") as file:
self.__data = file.read()
self.__ec_numbers = [
ec.group(1) for ec in re.finditer("(?<=ID\\t)(.*)(?=\\n)", self.__data)
Expand Down Expand Up @@ -262,8 +261,8 @@ def getReferencesDict(self):
lines = self.__getDataLines("RF")
for line in lines:
line = self.__removeTabs(line)
line, refs = self.__extractDataField(line, ("<", ">"))
references[refs[0]] = line
line, refs = self.__extractDataField(line, ('<', '>'))
references[refs] = line
return references

def printReactionSummary(self):
Expand Down