diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0f6c63c..9859c31 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,6 +35,7 @@ jobs: cd .. - name: Run tests run: | + PATH=$PATH:$HOME/local/bin make test.fast test-full: runs-on: macos-latest @@ -57,7 +58,6 @@ jobs: - name: Install HMMER run: | brew install hmmer - phmmer --version - name: Install MCL run: | mkdir installmcl diff --git a/orthohmm/__init__.py b/orthohmm/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/orthohmm/__main__.py b/orthohmm/__main__.py new file mode 100644 index 0000000..a518b7a --- /dev/null +++ b/orthohmm/__main__.py @@ -0,0 +1,6 @@ +"""orthohmm.__main__: executed when orthohmm is called as script""" +import sys + +from .orthohmm import main + +main(sys.argv[1:]) diff --git a/orthohmm/parser.py b/orthohmm/parser.py index 055cd42..f56e00c 100644 --- a/orthohmm/parser.py +++ b/orthohmm/parser.py @@ -134,9 +134,10 @@ def create_parser() -> ArgumentParser: orthohmm_single_copy_orthogroups A directory of FASTA files wherein each file is a single-copy ortholog. - Headers are modified to have taxon names come before the gene identifier. Taxon names are the file name - excluding the extension. Taxon name and gene identifier are separated by a pipe symbol "|". - This aims to help streamline phylogenomic workflows wherein sequences will be concatenated downstream + Headers are modified to have taxon names come before the gene identifier. + Taxon names are the file name excluding the extension. Taxon name and gene + identifier are separated by a pipe symbol "|". This aims to help streamline + phylogenomic workflows wherein sequences will be concatenated downstream based on taxon names. """ # noqa ),