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makefile
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# Enrichemt Analysis
PY := python3
run_go:
@echo RUN AN ENRICHMENT ANALYSIS EXAMPLE
$(PY) src/bin/run_enrichment.py data/exgo/study data/exgo/population data/exgo/association -m fdr_bh --pval=0.05 --pval_field=fdr_bh
run_m:
src/bin/run_enrichment.py data/exgo/study data/exgo/population data/exgo/association -m bonferroni,sidak,holm-sidak,holm,simes-hochberg,hommel,fdr_bh,fdr_by,fdr_tsbh,fdr_tsbky
run:
src/bin/run_enrichment.py data/ex/study001.txt data/ex/population.txt data/ex/population.txt
pylint:
@git status -uno | perl -ne 'if (/(\S+.py)/) {printf "echo $$1\npylint -r no %s\n", $$1}' | tee tmp_pylint
chmod 755 tmp_pylint
tmp_pylint
vim_:
vim -p \
src/bin/run_enrichment.py \
src/enrichmentanalysis/enrich_run.py \
src/enrichmentanalysis/enrich_rec.py \
src/enrichmentanalysis/enrich_results.py \
src/enrichmentanalysis/report_results.py \
src/enrichmentanalysis/file_utils.py \
src/enrichmentanalysis/multiple_testing.py \
src/enrichmentanalysis/pvalcalc.py \
src/enrichmentanalysis/wr_tbl.py \
src/enrichmentanalysis/wr_tbl_class.py \
src/enrichmentanalysis/cli.py \
src/tests/test_enrichment0.py
# --------------------------------------------------------------------------------
# Modify version in src/enrichmentanalysis/__init__.py
vim_pip:
vim -p src/enrichmentanalysis/__init__.py setup.py makefile
bdist_wheel:
#python3 -m pip install --user --upgrade setuptools wheel
make clean_dist
python3 setup.py sdist bdist_wheel
ls -lh dist
upload_pip:
python3 -m twine upload dist/* --verbose
bdist_conda:
python setup.py bdist_conda
# Test in a virtual environment
prep_conda:
conda remove --name myenv --all
conda create --name myenv
# conda activate myenv
# conda install -c dvklopfenstein enrichmentanalysis_dvklopfenstein
# run_enrichment.py
# run_enrichment.py data/exgo/study data/exgo/population data/exgo/association
tags:
git log --decorate=full --simplify-by-decoration --pretty=oneline HEAD
git tag -l -n
# --------------------------------------------------------------------------------
upload_pypi_test:
python setup.py register -r pypitest
python setup.py sdist upload -r pypitest
clean_dist:
rm -rf dist build enrichmentanalysis.egg-info
clean_pyc:
find . -name \*.pyc | xargs rm -f
find . -name \*.st\*p | xargs rm -f
clean:
rm -f enrichment.xlsx
rm -f *.csv
rm -f tmp_pylint
# Copyright (C) 2015-2019, DV Klopfenstein. All rights reserved.