153 bgc mappings generation (#155)

* change BGC attributes type from list to tuple

The following BGC attributes are updated:
- product_prediction
- mibig_bgc_class
- smiles

* use positional-only parameter in BGC and GCF

Parameters before "/" are positional-only parameters, see https://docs.python.org/3/glossary.html#term-parameter.

* update BGC's `__eq__` and `__hash__`

* update GCF's `__eq__` and `__hash__`

* Update gcf.py

* update Spectrum's `__eq__` and `__hash__`

* update MolecularFamily `__eq__` and `__hash__`

* Update molecular_family.py

* update Strain `__eq__` and `__hash__`

* update StrainCollection `__eq__`

* add TODO comments to ObjectLink

* add parameter type check for `add_alias`

* add `__contains__` to Strain class

* update `lookup` method of StrainCollection

* update `__contains__` in StrainCollection

* remove from __eq__

* update `__eq__` logic for Strain

* rename `_strain_dict_id` to `_strain_dict_name` in StrainCollection

* add comments to `get_common_strains`

* add comments and rename variables for DataLinks

* add comment about `met_only` parameter

* add todo comments to LinkFinder

* add comments to GNPSSpectrumLoader

to figure out how `spectrum_id` is set

* change Spectrum.spectrum_id from type int to str

* update spec_dict

* Update tests

* update `__eq__` in MolecularFamily

* change `MolecularFamily.family_id` from type int to str

* add method `has_strain` to MolecularFamily

* Update metcalf_scoring.py

* change array to dataframe in DataLinks

1. Change array to dataframe:
- self.M_gcf_strain -> self.gcf_strain_occurrence
- self. M_spec_strain -> self.spec_strain_occurrence
- self. M_fam_strain -> mf_strain_occurrence
2. update relevant methods to get the new dataframes
3. update logics of method `common_strains` using the new dataframes

* update references of the new dataframes from DataLinks

* update logics of `get_links` in NPLinker class

* Update test_nplinker.py

- add code to remove cached results

* move SCORING_METHODS to LinkFinder

* update method name to `get_common_strains`

* refactor mapping dataframes in DataLinks

* add TODOs and deprecation to LinkFinder

* refactor cooccurrence in DataLinks

* merge `load_data` and `find_correlations` to init in DataLinks

* refactor DataLinks attributes

- Move assignment of attributes to `__init__`
- Rename attributes
- Replace `fam` or `molfam` with `mf` to refer to molecular family
- Add docstrings

* Delete test_data_links.py

* update get_common_strains methods

- update parameters to be more clear and specific
- change strain id in returned dict to strain objects
-  update docstrings

* remove lookup_index method from StrainCollection (#90)

- remove method `lookup_index`
- remove attribute `_strain_dict_index`

* Remove integer id from GCF

* update lookup methods and attributes in NPLikner class

* change cooccurrence from array to DataFrame in DataLinks

* format link_finder.py

* temp replace array with dataframe in LinkFinder for metcalf scoring

* refactor `LinkFinder.get_scores` method

* refactor `LinkFinder.metcalf_scoring` method

- rename parameter name
- wrap parameters for weights to one parameter
- extract private method `_cal_mean_std`

* refactor get_links

* remove unused methods and scorings from LinkFinder

-  remove unused `likescore` and `hg` scoring types
- remove all unused methods

* refactor returned type of `LinkFinder.get_links` method

* add `lookup_mf` method in NPLinker class

* refactor MetcalfScoring class

* add deprecation to LinkLikelihood class

* add `__init__.py` to linking module

* rename `data_linking.py` to `data_links.py`

* rename `data_linking_functions.py` to `utils.py`

* rename `test_data_linking_functions.py` to `test_linking_utils.py`.py

* Delete test_scoring.py

* add dtype to DataLinks dataframes

* remove mapping dataframes and relevant method from DataLinks

Removed:
- self.mapping_spec
- self.mapping_gcf
- self.mapping_fam
-self.mapping_strain
- _get_mappings_from_occurrence() method

* Create test_data_links.py

* add `conftest.py` for scoring tests

* update LinkFinder's attribute and private method

- refactor method `_cal_mean_std`
- rename attribute `raw_score_fam_gcf` to `raw_score_mf_gcf`

* Create test_link_finder.py

* Update vscode plugin autodocstring template

- fix indentation bug in autodocsting
- remove `Examples:` section

* add scope for fixtures

* Create test_metcalf_scoring.py

* add docstrings and type hints to `MetcalfScoring` class

* add util func `isinstance_all`

* replace `_isinstance` with util func `isinstance_all`

* update validation of args for `DataLinks`

* Update test_data_links.py

- add docstrings
- add more tests

* add type hints for returned values to unit tests

* update exception types for invalid input

* add docstrings and type hints to `LinkFinder` class

* add more unit tests for `LinkFinder`

* fix input type bug for `DataLinks.get_common_strains`

* Create test_nplinker_scoring.py

* add todo comments to `NPLinker` class

* remove local integration tests for scoring part of `NPLinker`

- rename `test_nplinker.py` to `test_nplinker_local.py`

* remove unused imports

* Fix mypy warnings as much as possible

* check strain existence using strain dict

* change calculate abbrevation from "cal" to "calc"

* remove resolved TODO comment

* move shared fixtures to conftest.py

* remove unnecessary type hints

* update docstrings for cooccurrences

* use uuid for singleton molecular families #144

* add TODO comment for GNPSLoader

* fix typos

* remove useless parameter `met_only`

The `met_only` is useless. NPlinker will stop working if met_only=True.

* update exception type

* refactor the usage of PODPDownloader

1. create instance in the private method, only when it's needed
2. change the scope of the instance from global to local

* rename private config attributes in class DatasetLoader

-  add prefix `_config` for all config attributes
- add comments to restructure `__init__` code

* change the variable of app data dir to be global

this variable is independent of DatasetLoader and other classes, so it should be a global variable

* change two public methods to variables

* change one public method to attribute for DatasetLoader

* add value validation to Config

- move the validation of antismash format config in DatasetLoader to Config class
- refactor the config data validations into a private method

* add TODO comments about init and validate paths

* remove unused attribute `growth_media`

* remove commented code

* add TODO comments

* remove unused imports

* format the code

* reorder methods in loader.py

* add function `generate_genome_bgc_mappings_file`

* Update __init__.py

* add tests for `generate_genome_bgc_mappings_file`

* update strain test when 113 issue is closed

src/nplinker/genomics/__init__.py

@@ -1,22 +1,26 @@
 import logging
-
 from .abc import BGCLoaderBase
 from .bgc import BGC
 from .gcf import GCF
 from .genomics import filter_mibig_only_gcf
+from .genomics import generate_genome_bgc_mappings_file
+from .genomics import GENOME_BGC_MAPPINGS_FILENAME
 from .genomics import get_bgcs_from_gcfs
 from .genomics import get_strains_from_bgcs
 from .genomics import load_gcfs
 from .genomics import map_bgc_to_gcf
 from .genomics import map_strain_to_bgc
 
+
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __all__ = [
     "BGCLoaderBase",
     "BGC",
     "GCF",
     "filter_mibig_only_gcf",
+    "generate_genome_bgc_mappings_file",
+    "GENOME_BGC_MAPPINGS_FILENAME",
     "get_bgcs_from_gcfs",
     "get_strains_from_bgcs",
     "load_gcfs",

src/nplinker/genomics/genomics.py

@@ -1,16 +1,62 @@
 from __future__ import annotations
 import csv
+import json
 from os import PathLike
 from pathlib import Path
 from deprecated import deprecated
 from nplinker.logconfig import LogConfig
 from nplinker.strain_collection import StrainCollection
+from nplinker.utils import list_dirs
+from nplinker.utils import list_files
 from .bgc import BGC
 from .gcf import GCF
 
 
 logger = LogConfig.getLogger(__name__)
 
+GENOME_BGC_MAPPINGS_FILENAME = "genome_bgc_mappings.json"
+
+
+def generate_genome_bgc_mappings_file(bgc_dir: str | PathLike) -> None:
+    """Generate a file that maps genome id to BGC id.
+
+    The output file is named in variable `GENOME_BGC_MAPPINGS_FILENAME` and
+    is placed in the same directory as `bgc_dir`. The file will be overwritten
+    if it already exists.
+
+    Args:
+        bgc_dir(str | PathLike): The directory has one-layer of subfolders and
+            each subfolder contains BGC files in `.gbk` format.
+            It assumes that
+            - the subfolder name is the genome id (e.g. refseq),
+            - the BGC file name is the BGC id.
+    """
+    bgc_dir = Path(bgc_dir)
+    genome_bgc_mappings = {}
+
+    for subdir in list_dirs(bgc_dir):
+        genome_id = Path(subdir).name
+        bgc_files = list_files(subdir, suffix=(".gbk"), keep_parent=False)
+        bgc_ids = [
+            bgc_id for f in bgc_files if (bgc_id := Path(f).stem) != genome_id
+        ]
+        genome_bgc_mappings[genome_id] = bgc_ids
+
+    # sort mappings by genome_id and construct json data
+    genome_bgc_mappings = dict(sorted(genome_bgc_mappings.items()))
+    json_data = [{
+        "genome_ID": k,
+        "BGC_ID": v
+    } for k, v in genome_bgc_mappings.items()]
+    json_data = {
+        "mappings": json_data,
+        "count": len(json_data),
+        "version": "1.0"
+    }
+
+    with open(bgc_dir / GENOME_BGC_MAPPINGS_FILENAME, "w") as f:
+        json.dump(json_data, f)
+
 
 def map_strain_to_bgc(strains: StrainCollection, bgcs: list[BGC],
                       bgc_genome_mapping: dict[str, str]):
@@ -36,7 +82,8 @@ def map_strain_to_bgc(strains: StrainCollection, bgcs: list[BGC],
             genome_id = bgc_genome_mapping[bgc.bgc_id]
         except KeyError as e:
             raise KeyError(
-                f"Not found BGC id {bgc.bgc_id} in BGC-genome mappings.") from e
+                f"Not found BGC id {bgc.bgc_id} in BGC-genome mappings."
+            ) from e
         try:
             strain = strains.lookup(genome_id)
         except KeyError as e:

tests/genomics/test_genomics.py

@@ -1,14 +1,43 @@
 from __future__ import annotations
+import json
 import pytest
 from nplinker.genomics import BGC
 from nplinker.genomics import filter_mibig_only_gcf
 from nplinker.genomics import GCF
+from nplinker.genomics import generate_genome_bgc_mappings_file
+from nplinker.genomics import GENOME_BGC_MAPPINGS_FILENAME
 from nplinker.genomics import get_bgcs_from_gcfs
 from nplinker.genomics import get_strains_from_bgcs
 from nplinker.genomics import map_bgc_to_gcf
 from nplinker.genomics import map_strain_to_bgc
 from nplinker.strain_collection import StrainCollection
 from nplinker.strains import Strain
+from .. import DATA_DIR
+
+
+def test_generate_genome_bgc_mappings_file():
+    bgc_dir = DATA_DIR / "antismash"
+
+    generate_genome_bgc_mappings_file(bgc_dir)
+
+    with open(bgc_dir / GENOME_BGC_MAPPINGS_FILENAME) as f:
+        mappings = json.load(f)
+
+    assert mappings["count"] == 2
+
+    assert mappings["mappings"][0]["genome_ID"] == "GCF_000514515.1"
+    assert len(mappings["mappings"][0]["BGC_ID"]) == 20
+    for bgc_id in ["NZ_AZWB01000005.region001", "NZ_KI911412.1.region001"]:
+        assert bgc_id in mappings["mappings"][0]["BGC_ID"]
+    assert "GCF_000514515.1" not in mappings["mappings"][0]["BGC_ID"]
+
+    assert mappings["mappings"][1]["genome_ID"] == "GCF_000514855.1"
+    assert len(mappings["mappings"][1]["BGC_ID"]) == 24
+    for bgc_id in ["NZ_AZWS01000001.region001", "NZ_KI911483.1.region001"]:
+        assert bgc_id in mappings["mappings"][1]["BGC_ID"]
+    assert "GCF_000514855.1" not in mappings["mappings"][1]["BGC_ID"]
+
+    (bgc_dir / GENOME_BGC_MAPPINGS_FILENAME).unlink()
 
 
 @pytest.fixture
@@ -131,6 +160,4 @@ def test_get_strains_from_bgcs(strain_collection, bgc_list,
     map_strain_to_bgc(strain_collection, bgc_list, bgc_genome_mapping)
     strains = get_strains_from_bgcs(bgc_list)
     assert isinstance(strains, StrainCollection)
-    for strain in strain_collection:
-        assert strain in strains
-    # assert strains == strain_collection # use it when issue #113 is solved
+    assert strains == strain_collection