Klifs #58
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Klifs #58
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… KLIFS regions after reviewing structurally alignments manually and updated iterate_klifs_alignment function accordingly; started movign KLIFSPocket dataclass into klifs module
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
Resolved conflicts from pre-commit.ci
…Model that is included in Kinase object
…name; then converted search in database notebook to UniProt ID instead of HGNC gene name
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…of databases and Pydantic model generation; updated databases notebook and source files in data dir
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
…of databases and Pydantic model generation; updated databases notebook and source files in data dir rebased kinase schema
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
…ion, and all other remaining partial alignments
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…h a generator validation function for the latter
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jessicaw9910
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Oct 17, 2024
* simplified DICT_POCKET_KLIFS_REGIONS, have added notion of contiguous KLIFS regions after reviewing structurally alignments manually and updated iterate_klifs_alignment function accordingly; started movign KLIFSPocket dataclass into klifs module * adjusted KLIFS pocket notebook to adapt to klifs module changes * adjusted KLIFS pocket notebook to adapt to klifs module changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * flake8 fix for unused import * added initial find_start_or_end_recursively function * added initial kinase Pydantic schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * latest kinase Pydantic schema Resolved conflicts from pre-commit.ci * added csv files to data and updated database notebook * caching latest klifs pocket notebook * refactored model schema so that each database module has its own BaseModel that is included in Kinase object * klifs * updated KinaseInfo to use more general search term in lieu of kinase name; then converted search in database notebook to UniProt ID instead of HGNC gene name * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed F401 and F722 errors in kinase_schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir rebased kinase schema * used Kincore2UniProtAligner from aligment module in kincore module * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reverting to previous changes lost in rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed E266 flake8 error * started adding b.l alignment * added get_repo_root util lost after last rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added validation to fix incorrect KLIFS pocket for ADCK3 * used Self instead of self for ADCK3 KLIFS pocket validation fix * final commit before moving all functions to KLIFSPocket class * interim commit of klifs_pocket notebook while debugging bl alignment algorithm * added SO link to ADCK3 validator for future reference * added matplotlib_venn in dependencies * added validation correction for LRRK2 and CAMKK1 KLIFS pockets * finalized alignment algorithm for b.l, multi-matching post-concatenation, and all other remaining partial alignments * final notebook including partial alignment issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed extraneous dev code from klifs_pocket notebook * removed TODO from completed KLIFS tasks * added biopython to devtools test env for CI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * deleted unnecessary commented out code * removed commented out code now integrated into return_idx_of_alignment_match * added generate_alignment to KLIFSPocket and added to pre-init * added bool_offset and KLIFS2UniProt to KinaseInfo BaseModel along with a generator validation function for the latter * updated KLIFS pocket notebook for latest kinase schema including KLIFS2UniProt dict * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
jessicaw9910
added a commit
that referenced
this pull request
Oct 17, 2024
* separating out CI badges given monorepo structure * changed repo extension configuration * changed max depth given monorepo * added [tool.setuptools.packages.find] / where = [.] to databases pyproject.toml * pip install sub-package in readthedocs.yml; may also need to change docs/requirements.txt * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated sphinx-rtd-theme in requirements.txt * moved requirements.txt forward in readthedocs.yml * added docs packages to requirements.yaml since requirements.txt seeming to be ignored * fixed getting started code block * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * excluding tests * fixed inline code * max depth 3 * updated to exclude tests directories and contents * instantiation of experiments subpackage * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] pre-commit autoupdate (#61) updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/psf/black: 24.4.2 → 24.8.0](psf/black@24.4.2...24.8.0) - [github.com/PyCQA/flake8: 7.1.0 → 7.1.1](PyCQA/flake8@7.1.0...7.1.1) - [github.com/asottile/pyupgrade: v3.16.0 → v3.17.0](asottile/pyupgrade@v3.16.0...v3.17.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Klifs (#58) * simplified DICT_POCKET_KLIFS_REGIONS, have added notion of contiguous KLIFS regions after reviewing structurally alignments manually and updated iterate_klifs_alignment function accordingly; started movign KLIFSPocket dataclass into klifs module * adjusted KLIFS pocket notebook to adapt to klifs module changes * adjusted KLIFS pocket notebook to adapt to klifs module changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * flake8 fix for unused import * added initial find_start_or_end_recursively function * added initial kinase Pydantic schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * latest kinase Pydantic schema Resolved conflicts from pre-commit.ci * added csv files to data and updated database notebook * caching latest klifs pocket notebook * refactored model schema so that each database module has its own BaseModel that is included in Kinase object * klifs * updated KinaseInfo to use more general search term in lieu of kinase name; then converted search in database notebook to UniProt ID instead of HGNC gene name * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed F401 and F722 errors in kinase_schema * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * completed intial version of kinase_schema to allow for harmonization of databases and Pydantic model generation; updated databases notebook and source files in data dir rebased kinase schema * used Kincore2UniProtAligner from aligment module in kincore module * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reverting to previous changes lost in rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed E266 flake8 error * started adding b.l alignment * added get_repo_root util lost after last rebase * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added validation to fix incorrect KLIFS pocket for ADCK3 * used Self instead of self for ADCK3 KLIFS pocket validation fix * final commit before moving all functions to KLIFSPocket class * interim commit of klifs_pocket notebook while debugging bl alignment algorithm * added SO link to ADCK3 validator for future reference * added matplotlib_venn in dependencies * added validation correction for LRRK2 and CAMKK1 KLIFS pockets * finalized alignment algorithm for b.l, multi-matching post-concatenation, and all other remaining partial alignments * final notebook including partial alignment issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed extraneous dev code from klifs_pocket notebook * removed TODO from completed KLIFS tasks * added biopython to devtools test env for CI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * deleted unnecessary commented out code * removed commented out code now integrated into return_idx_of_alignment_match * added generate_alignment to KLIFSPocket and added to pre-init * added bool_offset and KLIFS2UniProt to KinaseInfo BaseModel along with a generator validation function for the latter * updated KLIFS pocket notebook for latest kinase schema including KLIFS2UniProt dict * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * added KinCore FASTA sequence file * updated data README to summarize how the csv files were generated and how the Pydantic models can be assembled * fixed KLIFS README * added trailing space README * pip install sub-package in readthedocs.yml; may also need to change docs/requirements.txt * moved requirements.txt forward in readthedocs.yml * push to trigger README reformat * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mark Polk <mark.polk@choderalab.org>
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Description
Solve partial alignments (e.g., b.l region) and non-contiguous adjacent region issues (e.g., III:aC) in KLIFS pocket
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