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Makefile
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## Run alignment-based functions
run.alignment_length:
python3 -m phykit-runner alignment_length ./tests/sample_files/simple.fa
run.alignment_length_no_gaps:
python3 -m phykit-runner alignment_length_no_gaps ./tests/sample_files/simple.fa
run.gc_content:
python3 phykit-runner.py gc_content ./tests/sample_files/simple.fa
run.pairwise_identity:
python3 phykit-runner.py pairwise_identity ./tests/sample_files/simple.fa
run.parsimony_informative_sites:
python3 -m phykit-runner parsimony_informative_sites ./tests/sample_files/simple.fa
run.rename_fasta_entries:
python3 phykit-runner.py rename_fasta_entries ./tests/sample_files/simple.fa -i tests/sample_files/simple_fasta_idmap.txt
run.rcv:
python3 -m phykit-runner rcv ./tests/sample_files/simple.fa
run.variable_sites:
python3 -m phykit-runner variable_sites ./tests/sample_files/simple.fa
## Run tree-based functions
run.bipartition_support_stats:
python3 -m phykit-runner bipartition_support_stats ./tests/sample_files/small_Aspergillus_tree.tre
run.branch_length_multiplier:
python3 phykit-runner.py branch_length_multiplier ./tests/sample_files/tree_simple.tre -f 2
run.collapse_branches:
python3 phykit-runner.py collapse_branches ./tests/sample_files/small_Aspergillus_tree.tre -s 100
run.covarying_evolutionary_rates:
python3 phykit-runner.py covarying_evolutionary_rates ./tests/sample_files/tree_simple.tre ./tests/sample_files/tree_simple_1.tre -r ./tests/sample_files/tree_simple_2.tre
run.dvmc:
python3 -m phykit-runner dvmc -t ./tests/sample_files/tree_simple.tre -r ./tests/sample_files/tree_simple.outgroup.txt
run.internal_branch_stats:
python3 -m phykit-runner internal_branch_stats ./tests/sample_files/tree_simple.tre
run.internode_labeler:
python3 -m phykit-runner internode_labeler ./tests/sample_files/tree_simple.tre
run.lb_score:
python3 -m phykit-runner lb_score ./tests/sample_files/tree_simple.tre
run.patristic_distances:
python3 -m phykit-runner patristic_distances ./tests/sample_files/tree_simple.tre
run.polytomy_test:
python3 phykit-runner.py polytomy_test -t ./tests/sample_files/test_trees.txt -g ./tests/sample_files/test_trees_groups.txt
run.print_tree:
python3 -m phykit-runner print_tree ./tests/sample_files/tree_simple.tre
run.prune_tree:
python3 phykit-runner.py prune ./tests/sample_files/tree_simple.tre ./tests/sample_files/tree_simple_prune.txt
run.rename_tree_tips:
python3 phykit-runner.py rename_tree_tips ./tests/sample_files/tree_simple.tre -i ./tests/sample_files/tree_simple_idmap.txt
run.rf_distance:
python3 -m phykit-runner rf_distance ./tests/sample_files/tree_simple.tre ./tests/sample_files/tree_simple_other_topology.tre
run.saturation:
python3 phykit-runner.py saturation -t ./tests/sample_files/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile -a ./tests/sample_files/12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit
run.spurious_sequence:
python3 -m phykit-runner spurious_sequence ./tests/sample_files/tree_simple.tre
run.tip_labels:
python3 -m phykit-runner tip_labels ./tests/sample_files/tree_simple.tre
run.total_tree_length:
python3 -m phykit-runner total_tree_length ./tests/sample_files/tree_simple.tre
run.treeness:
python3 -m phykit-runner treeness ./tests/sample_files/Yeasts_2832_eMRC_reference_renamed.tree
run.treeness_over_rcv:
python3 -m phykit-runner treeness_over_rcv -t ./tests/sample_files/tree_simple.tre -a ./tests/sample_files/simple.fa
## Helper commands
run.create_concatenation_matrix:
python3 phykit-runner.py create_concatenation_matrix -a tests/sample_files/alignment_list_for_create_concat_matrix.txt -p test
run.thread_dna:
python3 -m phykit-runner thread_dna -p ./tests/sample_files/EOG091N44MS.fa.mafft -n ./tests/sample_files/EOG091N44MS.fa
## Install, develop, and testing make commands
install:
# install so phykit command is available in terminal
python setup.py install
develop:
# https://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode
python setup.py develop
test: test.unit test.integration
test.unit:
python3 -m pytest -m "not integration"
test.integration:
rm -rf output/
mkdir output/
python3 -m pytest --basetemp=output -m "integration"
rm test.fa test.occupancy test.partition
test.fast:
python -m pytest -m "not (integration or slow)"
rm -rf output/
mkdir output/
python -m pytest --basetemp=output -m "integration and not slow" -vv
rm test.fa test.occupancy test.partition
# used by GitHub actions during CI workflow
test.coverage: coverage.unit coverage.integration
coverage.unit:
python -m pytest --cov=./ -m "not integration" --cov-report=xml:unit.coverage.xml
coverage.integration:
rm -rf output/
mkdir output/
python -m pytest --basetemp=output --cov=./ -m "integration" --cov-report=xml:integration.coverage.xml