From acb9eb94bd7dc5928b6221c3de0bcf0187202ae7 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 28 May 2020 11:52:21 +0200
Subject: [PATCH] xxxxxx_curation -> curation_tool
---
README.md | 10 +++++-----
bin/{gisaid_curation => curation_tool} | 10 +++++-----
curation_tool/__init__.py | 3 +++
{gisaid_curation => curation_tool}/common.py | 0
{gisaid_curation => curation_tool}/data_curation.py | 6 +++---
.../finalization_curation.py | 0
{gisaid_curation => curation_tool}/seq_curation.py | 2 +-
{gisaid_curation => curation_tool}/utils.py | 0
gisaid_curation/__init__.py | 3 ---
setup.py | 10 +++++-----
10 files changed, 22 insertions(+), 22 deletions(-)
rename bin/{gisaid_curation => curation_tool} (96%)
create mode 100644 curation_tool/__init__.py
rename {gisaid_curation => curation_tool}/common.py (100%)
rename {gisaid_curation => curation_tool}/data_curation.py (99%)
rename {gisaid_curation => curation_tool}/finalization_curation.py (100%)
rename {gisaid_curation => curation_tool}/seq_curation.py (99%)
rename {gisaid_curation => curation_tool}/utils.py (100%)
delete mode 100644 gisaid_curation/__init__.py
diff --git a/README.md b/README.md
index 714dce7..47cb382 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Help for GISAID curation process
+# Help for curation process
**Disclaimer:** This software is distributed as it is. Please double-check the results.
If you encounter any bug/miss-correction, please put an issue on the github page, or send pull-requests!
@@ -14,7 +14,7 @@ Python3 with pip (pip3).
Clone repository:
- git clone git@gitlab.pasteur.fr:aperrin/gisaid_curation.git
+ git clone git@gitlab.pasteur.fr:aperrin/curation_tool.git
Then:
@@ -45,15 +45,15 @@ new-born software until it is more stable). For that, go to `gisaid-curation` fo
To run the script only on metadata, use:
- gisaid_curation -m 'path to metadata xls file'
+ curation_tool -m 'path to metadata xls file'
To run the full curation, use:
- gisaid_curation -m 'path metadata xls' -r 'path tsv covsurver report' -s 'path fasta'
+ curation_tool -m 'path metadata xls' -r 'path tsv covsurver report' -s 'path fasta'
For more information, type:
- gisaid_curation -h
+ curation_tool -h
diff --git a/bin/gisaid_curation b/bin/curation_tool
similarity index 96%
rename from bin/gisaid_curation
rename to bin/curation_tool
index 42e5241..ca1ea07 100644
--- a/bin/gisaid_curation
+++ b/bin/curation_tool
@@ -25,11 +25,11 @@
import sys
import shutil
-from gisaid_curation import utils
-from gisaid_curation import common
-from gisaid_curation import data_curation
-from gisaid_curation import seq_curation
-from gisaid_curation import finalization_curation
+from curation_tool import utils
+from curation_tool import common
+from curation_tool import data_curation
+from curation_tool import seq_curation
+from curation_tool import finalization_curation
if __name__ == '__main__':
diff --git a/curation_tool/__init__.py b/curation_tool/__init__.py
new file mode 100644
index 0000000..fea931a
--- /dev/null
+++ b/curation_tool/__init__.py
@@ -0,0 +1,3 @@
+"""curation_tool"""
+
+__version__ = 2.0
\ No newline at end of file
diff --git a/gisaid_curation/common.py b/curation_tool/common.py
similarity index 100%
rename from gisaid_curation/common.py
rename to curation_tool/common.py
diff --git a/gisaid_curation/data_curation.py b/curation_tool/data_curation.py
similarity index 99%
rename from gisaid_curation/data_curation.py
rename to curation_tool/data_curation.py
index c3b5422..487f6f7 100644
--- a/gisaid_curation/data_curation.py
+++ b/curation_tool/data_curation.py
@@ -30,8 +30,8 @@ import string
import logging
logger = logging.getLogger("GC.metadata")
-from gisaid_curation import utils
-from gisaid_curation import common
+from curation_tool import utils
+from curation_tool import common
def cure_metadata(file_in):
@@ -824,5 +824,5 @@ def check_coverage(line, cov_list, cov_problem):
if __name__ == '__main__':
parsed = utils.make_parser(sys.argv[1:])
metadata = parsed.xls_file
- logger = utils.init_logger(metadata, "gisaid_curation")
+ logger = utils.init_logger(metadata, "curation_tool")
cure_metadata(metadata)
diff --git a/gisaid_curation/finalization_curation.py b/curation_tool/finalization_curation.py
similarity index 100%
rename from gisaid_curation/finalization_curation.py
rename to curation_tool/finalization_curation.py
diff --git a/gisaid_curation/seq_curation.py b/curation_tool/seq_curation.py
similarity index 99%
rename from gisaid_curation/seq_curation.py
rename to curation_tool/seq_curation.py
index 54530b7..d94e614 100644
--- a/gisaid_curation/seq_curation.py
+++ b/curation_tool/seq_curation.py
@@ -25,7 +25,7 @@
import logging
logger = logging.getLogger("GC.covsurver")
-from gisaid_curation import common
+from curation_tool import common
def get_covsurver_info(cov_report, to_hand_back, vname_changes):
"""
diff --git a/gisaid_curation/utils.py b/curation_tool/utils.py
similarity index 100%
rename from gisaid_curation/utils.py
rename to curation_tool/utils.py
diff --git a/gisaid_curation/__init__.py b/gisaid_curation/__init__.py
deleted file mode 100644
index 9b814e6..0000000
--- a/gisaid_curation/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""gisaid_curation"""
-
-__version__ = 2.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 8a5d74f..4e58f0b 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
Setup script
"""
-import gisaid_curation
+import curation_tool
try:
from setuptools import setup
from setuptools.command.test import test as TestCommand
@@ -38,9 +38,9 @@ def parse_requirements(requirements):
and not l.startswith('#')]
-packages = ['gisaid_curation']
+packages = ['curation_tool']
requires = parse_requirements("requirements.txt")
-scripts = ['bin/gisaid_curation']
+scripts = ['bin/curation_tool']
classifiers = [
"Environment :: Console",
@@ -55,9 +55,9 @@ with open('README.md') as f:
long_description = f.read()
setup(
- name='gisaid_curation',
+ name='curation_tool',
packages=packages,
- version=gisaid_curation.__version__,
+ version=curation_tool.__version__,
description="Helping for gisaid database curation of new submitted sequences",
long_description=long_description,
author='Amandine Perrin',
--
GitLab