Merge branch 'master' of github.com:saezlab/pypath

pypath/core/annot.py

@@ -6906,3 +6906,27 @@ def get_db(
         )
 
     return globals()['db']
+
+class HPO(AnnotationBase):
+
+    _eq_fields = ()
+
+    def __init__(self, **kwargs):
+        """
+        HPO Gene Annotations from the HPO database.
+        """
+
+        kwargs.pop('ncbi_tax_id', None)
+
+        AnnotationBase.__init__(
+            self,
+            name = 'HPO',
+            ncbi_tax_id = constants.NOT_ORGANISM_SPECIFIC,
+            input_method = 'hpo.hpo_annotations',
+            **kwargs
+        )
+
+    def _process_method(self):
+        #  already the appropriate format, no processing needed
+        self.annot = self.data
+        delattr(self, 'data')

pypath/data/licenses/hpo.json

@@ -0,0 +1,7 @@
+{
+    "name": "HPO",
+    "full_name": "HPO License",
+    "url": "https://hpo.jax.org/app/license",
+    "purpose": "academic",
+    "sharing": "alike"
+}

pypath/inputs/chembl.py

@@ -0,0 +1,346 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#
+#  This file is part of the `pypath` python module
+#
+#  Copyright
+#  2014-2022
+#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
+#
+#  Authors: Dénes Türei (turei.denes@gmail.com)
+#           Nicolàs Palacio
+#           Sebastian Lobentanzer
+#           Erva Ulusoy
+#           Olga Ivanova
+#           Ahmet Rifaioglu
+#           Tennur Kılıç
+#
+#  Distributed under the GPLv3 License.
+#  See accompanying file LICENSE.txt or copy at
+#      http://www.gnu.org/licenses/gpl-3.0.html
+#
+#  Website: http://pypath.omnipathdb.org/
+#
+
+from typing import Literal
+
+import json
+import collections
+
+import pypath.share.curl as curl
+import pypath.resources.urls as urls
+
+
+def chembl_targets() -> list[tuple]:
+    """
+    Retrieves targets data from ChEMBL.
+
+    Returns:
+        List of drug target records as named tuples.
+    """
+
+    fields_target = (
+        'accession',
+        'target_chembl_id',
+    )
+
+    ChemblTarget = collections.namedtuple(
+        'ChemblTarget',
+        fields_target,
+        defaults = (None,) * len(fields_target),
+    )
+
+    tgt_lst = []
+    page_dct = {}
+
+    while True:
+
+        if not page_dct:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{urls.urls['chembl']['target']}"
+            )
+
+        elif page_dct['page_meta']['next']:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{page_dct['page_meta']['next']}"
+            )
+
+        else:
+
+            break
+
+        c = curl.Curl(url, large=True, silent=False)
+        fileobj = open(c.fileobj.name)
+        page_dct = json.loads(fileobj.read())
+
+        tgt_lst.extend(
+            ChemblTarget(
+                accession = (
+                    tgt['target_components'][0]['accession']
+                        if tgt['target_components'] else
+                    None
+                ),
+                target_chembl_id = tgt['target_chembl_id'],
+            )
+            for tgt in page_dct['targets']
+        )
+
+    return tgt_lst
+
+
+def chembl_assays() -> list[tuple] :
+    """
+    Retrieves assays data from ChEMBL.
+
+    Returns:
+        List of assay records as named tuples.
+    """
+
+    fields_assay = (
+        'assay_chembl_id',
+        'assay_organism',
+        'assay_type',
+        'confidence_score',
+        'target_chembl_id',
+    )
+
+    ChemblAssay = collections.namedtuple(
+        'ChemblAssay',
+        fields_assay,
+        defaults = (None,) * len(fields_assay),
+    )
+
+    assay_lst = []
+    page_dct = {}
+
+    while True:
+
+        if not page_dct:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{urls.urls['chembl']['assay']}"
+            )
+
+        elif page_dct['page_meta']['next']:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{page_dct['page_meta']['next']}"
+            )
+
+        else:
+
+            break
+
+        c = curl.Curl(url, large=True, silent=False)
+        fileobj = open(c.fileobj.name)
+        page_dct = json.loads(fileobj.read())
+
+        assay_lst.extend(
+            ChemblAssay(
+                assay_chembl_id = assy_attr['assay_chembl_id'],
+                assay_organism = assy_attr['assay_organism'],
+                assay_type = assy_attr['assay_type'],
+                confidence_score = assy_attr['confidence_score'],
+                target_chembl_id = assy_attr['target_chembl_id'],
+            )
+            for assy_attr in page_dct['assays']
+        )
+
+    return assay_lst
+
+
+def chembl_molecules() -> list[tuple]:
+    """
+    Retrieves molecules data from ChEMBL.
+
+    Returns:
+        Molecule records as named tuples.
+    """
+
+    def _get(mol, key0, key1):
+
+        molecule_properties = mol.get(f'molecule_{key0}', {})
+
+        if molecule_properties:
+
+            return molecule_properties.get(key1, None)
+
+        else:
+
+            return None
+
+
+    fields_molecule = (
+        'alogp',
+        'canonical_smiles',
+        'chirality',
+        'full_mwt',
+        'heavy_atoms',
+        'std_inchi_key',
+        'species',
+        'type',
+        'chembl',
+        'parent_chembl',
+        'prodrug',
+        'std_inchi',
+        'xrefs',
+    )
+
+    ChemblMolecule = collections.namedtuple(
+        'ChemblMolecule',
+        fields_molecule,
+        defaults = (None,) * len(fields_molecule),
+    )
+
+    mol_lst = []
+    page_dct = {}
+
+    while True:
+
+        if not page_dct:
+
+            url = urls.urls['chembl']['url'] + urls.urls['chembl']['molecule']
+            c = curl.Curl(url, large=True, silent=False)
+
+        elif page_dct['page_meta']['next']:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{page_dct['page_meta']['next']}"
+            )
+
+        else:
+
+            break
+
+        c = curl.Curl(url, large=True, silent=False)
+        fileobj = open(c.fileobj.name)
+        page_dct = json.loads(fileobj.read())
+
+        mol_lst.extend(
+            ChemblMolecule(
+                chirality = mol['chirality'],
+                type = mol['molecule_type'],
+                prodrug = mol['prodrug'],
+
+                chembl = _get(mol, 'hierarchy', 'molecule_chembl_id'),
+                parent_chembl = _get(mol, 'hierarchy', 'parent_chembl_id'),
+
+                alogp = _get(mol, 'properties', 'alogp'),
+                full_mwt = _get(mol, 'properties', 'full_mwt'),
+                heavy_atoms = _get(mol, 'properties', 'heavy_atoms'),
+                species = _get(mol, 'properties', 'molecular_species'),
+
+                canonical_smiles = _get(mol, 'structures', 'canonical_smiles'),
+                std_inchi_key = _get(mol, 'structures', 'standard_inchi_key'),
+                std_inchi = _get(mol, 'structures', 'standard_inchi'),
+
+                xrefs = (
+                    [
+                        {
+                            'xref_id': rec['xref_id'],
+                            'xref_src': rec['xref_src'],
+                        }
+                        for rec in mol['cross_references']
+                    ]
+                        if mol['cross_references'] else
+                    None
+                )
+            )
+            for mol in page_dct['molecules']
+        )
+
+    return mol_lst
+
+
+def chembl_activities(
+        #TODO: are these below all the allowed values?
+        standard_relation: Literal['=', '>', '<', '>=', '<='],
+        pchembl_value_none: bool = False,
+    ) -> list[tuple] :
+    """
+    Retrieves activities data from ChEMBL.
+
+    Args:
+        pchembl_value_none:
+            # TODO: it is allowed to be None or must be None?
+            Whether the pchembl value should be none or not.
+        standard_relation:
+            Which standard relation in needed.
+
+    Returns:
+        List of activity records as named tuples. `standard_flag` and
+        `standard_units` attributes are not included in the returned records.
+        # TODO: then why the data_validity_comment is part of the records?
+        Only records without `data_validity_comment` are returned.
+    """
+
+    fields_activity = (
+        'assay_chembl',
+        'data_validity_comment',
+        'chembl',
+        'pchembl',
+        'standard_relation',
+        'standard_value',
+        'target_chembl',
+    )
+
+    ChemblActivity = collections.namedtuple(
+        'ChemblActivity',
+        fields_activity,
+        defaults = (None,) * len(fields_activity),
+    )
+
+    activity_lst = []
+    page_dct = {}
+
+    while True:
+
+        if not page_dct:
+
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{urls.urls['chembl']['activity']}"
+                f"&pchembl_value__isnull={str(pchembl_value_none).lower()}"
+                f"&standard_relation__exact={standard_relation}"
+            )
+
+        elif page_dct['page_meta']['next']:
+
+            url = (
+                f"{urls.urls['chembl']['url']}"
+                f"{page_dct['page_meta']['next']}"
+            )
+
+        else:
+
+            break
+
+        c = curl.Curl(url, large=True, silent=False)
+        fileobj = open(c.fileobj.name)
+        page_dct = json.loads(fileobj.read())
+
+
+        activity_lst.extend(
+            ChemblActivity(
+                assay_chembl = act['assay_chembl_id'],
+                data_validity_comment = act['data_validity_comment'],
+                chembl = act['molecule_chembl_id'],
+                pchembl = act['pchembl_value'],
+                standard_relation = act['standard_relation'],
+                standard_value = act['standard_value'],
+                target_chembl = act['target_chembl_id'],
+            )
+            for act in page_dct['activities']
+            if act['data_validity_comment'] is None
+        )
+
+    return activity_lst