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

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* flake8 fix for unused import

* added initial find_start_or_end_recursively function

* added initial kinase Pydantic schema

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* 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

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* 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

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* fixed F401 and F722 errors in kinase_schema

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* 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

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* reverting to previous changes lost in rebase

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* fixed E266 flake8 error

* started adding b.l alignment

* added get_repo_root util lost after last rebase

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* 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

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* removed extraneous dev code from klifs_pocket notebook

* removed TODO from completed KLIFS tasks

* added biopython to devtools test env for CI

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* 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

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

devtools/conda-envs/test_env.yaml

@@ -20,3 +20,4 @@ dependencies:
   - requests-cache
   - beautifulsoup4
   - numpy
+  - biopython

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/aligners.py

@@ -0,0 +1,45 @@
+from dataclasses import dataclass
+
+from Bio import Align
+
+
+@dataclass
+class CustomAligner:
+    mode: str = "local"
+    """str: Alignment mode. Default is "local"."""
+    substitution_matrix: str = "BLOSUM62"
+    """str: Substitution matrix. Default is BLOSUM62."""
+    gap_score: int = -5
+    """int: Gap score. Default is -5."""
+    extend_gap_score: int = -1
+    """int: Gap extension score. Default is -1."""
+
+    def __post_init__(self):
+        self.aligner = Align.PairwiseAligner()
+        self.aligner.mode = self.mode
+        self.aligner.substitution_matrix = Align.substitution_matrices.load(
+            self.substitution_matrix
+        )
+        self.aligner.open_gap_score = self.gap_score
+        self.aligner.extend_gap_score = self.extend_gap_score
+
+    def align(self, seq1: str, seq2: str) -> Align.MultipleSeqAlignment:
+        return self.aligner.align(seq1, seq2)
+
+
+@dataclass
+class BL2UniProtAligner(CustomAligner):
+    mode: str = "global"
+    """str: Alignment mode. Default is "global."""
+
+    def __post_init__(self):
+        super().__post_init__()
+
+
+@dataclass
+class Kincore2UniProtAligner(CustomAligner):
+    mode: str = "local"
+    """str: Alignment mode. Default is "local."""
+
+    def __post_init__(self):
+        super().__post_init__()