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makefile
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# Reactome Python Neo4j tasks
PY = python3
# pylint:
# git status -uno | perl -ne 'if (/(\S.*\S):\s+(\S+.py)/) {printf "echo $$1\npylint -r no %s\n", $$2}' | tee tmp_pylint
# chmod 755 tmp_pylint
# tmp_pylint
hello:
@echo "Welcome to ReactomePy"
g:
git status -uno
git remote -v
git branch
py:
find src -name \*.py
run:
src/bin/pwy_enrichment_reactome.py data/enrich/studyids/UniProt.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
run_tutorial:
$(PY) src/bin_neo4j/tutorial/fig4a_2018_molecules_in_interleukin_signaling.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/fig4b_2018_ccr5_pathways.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s1a_get_pathway.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s1b_get_protein.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s2a_get_protein_fields.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s2b_get_protein_fields_from_nodes.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s3a_get_participants_complexes.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s4a_pathway_subpathways.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s4b_pathway_superpathways.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s5a_pathway_reactions.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s6a_reaction_participants.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s6b_reaction_participants.py $(PASSWORD)
$(PY) src/bin_neo4j/tutorial/s7a_pathway_molecules.py $(PASSWORD)
# --------------------------------------------------------------------------------
# Re-generate Python modules containing Reatome data
# This is done for every new Reactome version
wrpy:
src/bin_neo4j/wrpy/species.py $(PASSWORD)
src/bin_neo4j/wrpy/disease.py $(PASSWORD)
src/bin_neo4j/wrpy/referencedatabase.py $(PASSWORD)
src/bin_neo4j/wrpy/inferredfrom.py $(PASSWORD)
src/bin_neo4j/wrpy/pathway_molecules.py $(PASSWORD)
# = TEST =========================================================================
tags:
git log --decorate=full --simplify-by-decoration --pretty=oneline HEAD
git tag -l -n
pytest:
python3 -m pytest -v src/tests | tee pytest.log
test:
make test_simple
test_simple:
$(PY) src/tests/rpt_figs.py
$(PY) src/tests/test_args_neo4j.py
$(PY) src/tests/test_args_pwyea_reactome.py
# = CLEAN ========================================================================
clean:
rm -f *.csv
rm -f *pathway_enrichment*.pdf
rm -f relationship_*.txt
rm -f tmp_pylint
make -f makefile clean_pyc
clean_tutorial:
rm -f fig4a_pathway_molecules_IL_sig_R-HSA-6785807.txt
rm -f fig4b_pathways_containing_CCR5.txt
rm -f complex_components_all.txt
rm -f pathway_molecules_R-HSA-983169.txt
clean_pyc:
find . -name \*.pyc | xargs rm -f
find . -name \*.st\*p | xargs rm -f
rm -f tmp
rm -f tmp_pylint
clobber_materials:
rm goa_human.*; wget http://geneontology.org/gene-associations/goa_human.gaf.gz; gunzip goa_human.gaf.gz
rm go-basic.obo*; wget http://geneontology.org/ontology/go-basic.obo
clobber_pwys:
rm -f src/reactomepy/data/*/pathways/p*.py
clean_dist:
rm -rf dist build reactomepy.egg-info
# Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved.