xxxxxx_curation -> curation_tool

README.md

-# 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
 
 
 

bin/gisaid_curation → 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__':

gisaid_curation/__init__.py → curation_tool/__init__.py

-"""gisaid_curation"""
+"""curation_tool"""
 
 __version__ = 2.0
\ No newline at end of file

gisaid_curation/data_curation.py → 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)

gisaid_curation/seq_curation.py → 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):
     """

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',