GraDiv 0.1.0__tar.gz

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Files changed (38) hide show
  1. gradiv-0.1.0/.gitignore +5 -0
  2. gradiv-0.1.0/.gitlab-ci.yml +34 -0
  3. gradiv-0.1.0/GraDiv.egg-info/PKG-INFO +763 -0
  4. gradiv-0.1.0/GraDiv.egg-info/SOURCES.txt +36 -0
  5. gradiv-0.1.0/GraDiv.egg-info/dependency_links.txt +1 -0
  6. gradiv-0.1.0/GraDiv.egg-info/entry_points.txt +5 -0
  7. gradiv-0.1.0/GraDiv.egg-info/requires.txt +6 -0
  8. gradiv-0.1.0/GraDiv.egg-info/top_level.txt +1 -0
  9. gradiv-0.1.0/LICENSE +674 -0
  10. gradiv-0.1.0/MANIFEST.in +2 -0
  11. gradiv-0.1.0/PKG-INFO +763 -0
  12. gradiv-0.1.0/README.rst +59 -0
  13. gradiv-0.1.0/gradiv/__init__.py +7 -0
  14. gradiv-0.1.0/gradiv/_version.py +21 -0
  15. gradiv-0.1.0/gradiv/algo.py +163 -0
  16. gradiv-0.1.0/gradiv/functions.py +91 -0
  17. gradiv-0.1.0/gradiv/main.py +241 -0
  18. gradiv-0.1.0/gradiv/pggraph.py +361 -0
  19. gradiv-0.1.0/gradiv/polymorphism.py +49 -0
  20. gradiv-0.1.0/gradiv/tests.py +17 -0
  21. gradiv-0.1.0/pyproject.toml +62 -0
  22. gradiv-0.1.0/setup.cfg +4 -0
  23. gradiv-0.1.0/test_data/figures/indels.png +0 -0
  24. gradiv-0.1.0/test_data/figures/inv.png +0 -0
  25. gradiv-0.1.0/test_data/figures/seminested.png +0 -0
  26. gradiv-0.1.0/test_data/figures/snps.png +0 -0
  27. gradiv-0.1.0/test_data/test_graph.gfa +113 -0
  28. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bam_files/test_graph.bam +0 -0
  29. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bam_files/test_graph.bam.bai +0 -0
  30. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bed_files/genome1.bed +23 -0
  31. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bed_files/genome2.bed +26 -0
  32. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bed_files/genome3.bed +27 -0
  33. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/bed_files/genome4.bed +24 -0
  34. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/header_test_graph.txt +1 -0
  35. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/links_test_graph.db +0 -0
  36. gradiv-0.1.0/test_data/test_graph_GraTools_INDEX/samples_chrom.txt +4 -0
  37. gradiv-0.1.0/test_data/test_graph_gradiv/test_graph_id_table.csv +14 -0
  38. gradiv-0.1.0/test_data/test_graph_gradiv/test_graph_seq_table.csv +14 -0
gradiv-0.1.0/.gitignore ADDED
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+ GraDiv.egg-info
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+ gradiv/__pycache__
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+ gradiv/_version.py
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+ gradiv/test*
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+ .idea/
gradiv-0.1.0/.gitlab-ci.yml ADDED
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+ # docker image used to build the app
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+ image: python:3.10
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+ stages:
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+ - install
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+ - test
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+ before_script:
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+ - echo ${CI_PROJECT_DIR}
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+ - echo ${CI_COMMIT_REF_NAME}
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+ - export PATH=$PATH:/root/.local/bin
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+ - python3 -m pip install -U setuptools build pip
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+ - python3 -m pip install --user gradiv@git+https://forge.ird.fr/phim/gradiv.git@$CI_COMMIT_REF_NAME
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+ test_install:
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+ stage: install
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+ script:
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+ - gradiv --help
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+ # tag:
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+ # - VM
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+ # rules:
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+ # - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # if commit tag starts with v
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+ # - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i" # test in commit message
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+ test_call:
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+ stage: test
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+ script:
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+ - mkdir gradiv_ci
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+ - cd gradiv_ci
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+ - git clone https://forge.ird.fr/phim/gradiv.git
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+ - gradiv call -g gradiv/test_data/test_graph_GraTools_INDEX
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+ test_compute:
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+ stage: test
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+ script:
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+ - mkdir gradiv_ci
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+ - cd gradiv_ci
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+ - git clone https://forge.ird.fr/phim/gradiv.git
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+ - gradiv compute -g gradiv/test_data/test_graph_GraTools_INDEX --stat-type site,unphased,phased