diff --git a/README.md b/README.md index 714dce7204c9f1ffa1b97d154bc44bacf49144c5..47cb3824077f34d0373d018d7198f3890c9db4ac 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 42e5241ec65357417f5e73c41b57fea1d0d1a648..ca1ea07b6bf4f9ef5ea26d97bccb79da82752b87 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 0000000000000000000000000000000000000000..fea931a745899b7a5b62894c7a372cff58045a07 --- /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 c3b542215837704758df23393dcaf1f2d49b368e..487f6f7ac6ddae62833de08601d5218a5ba0301e 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 54530b786a44a2ea0308bc3ed3057958a4b02df0..d94e614ef399228a420307a256474524243eb211 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 9b814e632177348501a7cce397636b11f588b32c..0000000000000000000000000000000000000000 --- 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 8a5d74f97b2fa2522b3030606a2ae1c96c120212..4e58f0bea2e6ffefdcc4befed9e94d1bd5f8d170 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',