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makefile
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# configuration for Gene Ontology files
GO_OBO_FILE=go-basic.obo
GOSLIM_OBO_FILE=goslim_generic.obo
GO_OBO_DOWNLOAD=http://geneontology.org/ontology/go-basic.obo
GOSLIM_OBO_DOWNLOAD=http://www.geneontology.org/ontology/subsets/goslim_generic.obo
GOEA_FILES = data/study data/population data/association
# Example GO: translation factor activity RNA binding
GO = GO:0008135
# -------------------------------------------------------------------------------
# ---- Sphinx-Generated Documentation -------------------------------------------
# -------------------------------------------------------------------------------
# GENERATE A TEMPORARY LOCAL WORKING COPY of Sphinx docs when developing documentation.
#
# User your browser to view the temporary local html files located at:
# <LOCAL_GIT_ROOT>/sphinx/_build/html/index.html
#
# Html files generated using "mkdocs_practice" should not be committed or pushed.
# Use the "mkdocs_live" or "gh-pages" make target to generate html docs
# which will be saved in the "goatools" "GitHub Pages".
# "GitHub Pages" are public webpages hosted and published through the goatools repository.
.PHONY: mkdocs rmdocs gh-pages
mkdocs_practice:
make -C sphinx/ apidoc html
# REMOVE THE TEMPORARY LOCAL WORKING COPY of Sphinx docs after a session of developing documentation.
rmdocs_practice:
make clean_docgen
# Update Live on-line GOATOOLS Documentation
mkdocs_live:
make gh-pages
# GENERATE SPHINX HTML DOCS DISPLAYED ON-LINE.
#
# Make target, "gh-pages" does the following:
# 1. Switches from the "master" branch to the "gh-pages" branch
# 2. While in the "gh-pages" branch, checks out from the "master" branch:
# a. Sphinx control files
# b. GOATOOLS source code, which contains docstrings
# The docstrings are used to create Sphinx html documentation
# 3. Creates html documentation using Sphinx in the "gh-pages" branch.
# 4. Commits and pushes html docs from "gh-pages" branch.
# 5. Switches back to the master branch
gh-pages:
git checkout gh-pages
git rm -rf .
git clean -dxf
git checkout HEAD .nojekyll
git checkout master sphinx goatools scripts
make -C sphinx/ apidoc html
mv -fv sphinx/_build/html/* .
mv -fv _apidoc/* .
rm -rf sphinx/ goatools/
git add -A
git commit -m "Generated gh-pages for `git log master -1 --pretty=short --abbrev-commit`"
git push
git checkout master
# -------------------------------------------------------------------------------
# ---- Run Scripts --------------------------------------------------------------
# -------------------------------------------------------------------------------
goea: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES)
goea_scipy_pval: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES) --pvalcalc fisher_scipy_stats
goea_basic: $(GO_OBO_FILE)
python scripts/find_enrichment.py $(GOEA_FILES)
goea_xlsx: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES) --outfile=goea.xlsx
goea_xlsx_bonferroni: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES) --method=bonferroni --outfile=goea_bonferroni.xlsx
goea_tsv: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES) --outfile=goea.tsv
goea_files: $(GO_OBO_FILE)
python scripts/find_enrichment.py --pval=0.05 --indent $(GOEA_FILES) --outfile=goea.tsv,goea.xlsx
plot_go_pygraphviz: $(GO_OBO_FILE)
python scripts/plot_go_term.py --term=$(GO)
plot_go_pydot: $(GO_OBO_FILE)
python scripts/plot_go_term.py --term=$(GO) --engine=pydot
map_slim: $(GO_OBO_FILE) $(GOSLIM_OBO_FILE)
python scripts/map_to_slim.py --association_file=data/association --slim_out=direct $(GO_OBO_FILE) $(GOSLIM_OBO_FILE)
goea_all: goea goea_basic goea_xlsx goea_xlsx_bonferroni goea_tsv goea_files
# if the gene ontology files don't exist, download them
$(GO_OBO_FILE):
@echo "downloading GO file: $(GO_OBO_FILE)"
wget -O $(GO_OBO_FILE) $(GO_OBO_DOWNLOAD)
$(GOSLIM_OBO_FILE):
@echo "downloading GOslim file: $(GOSLIM_OBO_FILE)"
wget -O $(GOSLIM_OBO_FILE) $(GOSLIM_OBO_DOWNLOAD)
clean:
rm -f goea*.xlsx goea.tsv GO_lineage.png
cd tests; make --no-print-directory clean
cd goatools; rm -f *.pyc
rm -f *.xlsx *.tsv *.log
rm -f nbt3102_*
# Removes local files in master branch generated using Sphinx
clean_docgen:
rm -rf ./_apidoc/
rm -rf ./_modules/
rm -rf ./_sources/
rm -rf ./_static/
rm -f genindex.html
rm -f index.html
rm -f objects.inv
rm -f py-modindex.html
rm -f search.html
rm -f searchindex.js
rm -rf sphinx/_apidoc/
rm -rf sphinx/_build/
rm -f fetch_associations.html
rm -f find_enrichment.html
rm -f goatools.html
rm -f map_to_slim.html
rm -f modules.html
rm -f plot_go_term.html
rm -f write_hierarchy.html
clobber:
@make --no-print-directory clean
rm -f $(GO_OBO_FILE) $(GOSLIM_OBO_FILE)
# TBD: Add these to NOSETEST after edits:
# tests/test_goea_local.py \
# tests/test_annotations_gaf.py \
# tests/test_altid_godag.py \
# tests/test_dnlds.py \
# tests/test_genes_cell_cycle.py \
# tests/test_go_print.py \
# tests/test_goea_errors.py \
# tests/test_goea_rpt_bonferroni.py \
# tests/test_nbt3102.py \
# tests/test_ncbi_entrez_annotations.py \
# tests/test_optional_fields.py \
# tests/test_write_hier.py \
# tests/test_pvalcalc.py \
# tests/test_wr_py_goea_results.py \
# tests/test_wr_tbl_subset.py \
# tests/test_write_summary_cnts.py
NOSETESTS := \
tests/test_combine_nt_lists.py \
tests/test_get_paths.py \
tests/test_get_unique_fields.py \
tests/test_go_draw.py \
tests/test_goea_statsmodels.py \
tests/test_mapslim.py
test:
nosetests tests/test_goea_statsmodels.py $(NOSETESTS)