Merge b3e5753 into d06b6e8

download.yaml

@@ -30,6 +30,9 @@
   # drug - target interactions from Drug Central
   url: http://unmtid-shinyapps.net/download/drug.target.interaction.tsv.gz
   local_name: drug.target.interaction.tsv.gz
+-
+  url: http://unmtid-shinyapps.net/download/tcrd.zip
+  local_name: tcrd.zip
 
 #
 # PPI from STRING DB

kg_covid_19/transform_utils/drug_central/drug_central.py

@@ -1,16 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
-
+import csv
 import gzip
 import logging
 import os
+import re
+import tempfile
+from collections import defaultdict
 
 from typing import Dict, List, Optional
 
 from kg_covid_19.transform_utils.transform import Transform
 from kg_covid_19.utils.transform_utils import write_node_edge_item, \
-    get_item_by_priority, ItemInDictNotFound, parse_header, data_to_dict
+    get_item_by_priority, ItemInDictNotFound, parse_header, data_to_dict, \
+    unzip_to_tempdir
 
 """
 Ingest drug - drug target interactions from Drug Central
@@ -27,6 +30,7 @@ class DrugCentralTransform(Transform):
     def __init__(self, input_dir: str = None, output_dir: str = None) -> None:
         source_name = "drug_central"
         super().__init__(source_name, input_dir, output_dir)  # set some variables
+        self.node_header = ['id', 'name', 'category', 'tclin', 'tchem']
 
     def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") -> None:
         """Method is called and performs needed transformations to process the Drug
@@ -35,6 +39,7 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
 
         interactions_file = os.path.join(self.input_base_dir,
                                          "drug.target.interaction.tsv.gz")
+        tclin_chem_zip_file = os.path.join(self.input_base_dir, "tcrd.zip")
         os.makedirs(self.output_dir, exist_ok=True)
         drug_node_type = "biolink:Drug"
         gene_curie_prefix = "UniProtKB:"
@@ -45,6 +50,13 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
         self.edge_header = ['subject', 'edge_label', 'object', 'relation',
                             'provided_by', 'comment']
 
+        # unzip tcrd.zip and get tchem and tclin filenames
+        tempdir = tempfile.mkdtemp()
+        (tclin_file, tchem_file) = unzip_and_get_tclin_tchem(tclin_chem_zip_file, tempdir)
+
+        tclin_dict: dict = tsv_to_dict(tclin_file, 'uniprot')
+        tchem_dict: dict = tsv_to_dict(tchem_file, 'uniprot')
+
         with open(self.output_node_file, 'w') as node, \
                 open(self.output_edge_file, 'w') as edge, \
                 gzip.open(interactions_file, 'rt') as interactions:
@@ -79,15 +91,22 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
                                      header=self.node_header,
                                      data=[drug_id,
                                            items_dict['DRUG_NAME'],
-                                           drug_node_type])
+                                           drug_node_type,
+                                           str(False),
+                                           str(False)])
 
                 for gene_id in gene_ids:
                     gene_id = gene_curie_prefix + gene_id
+                    is_tclin = True if gene_ids[0] in tclin_dict else False
+                    is_tchem = True if gene_ids[0] in tchem_dict else False
+
                     write_node_edge_item(fh=node,
                                          header=self.node_header,
                                          data=[gene_id,
                                                items_dict['GENE'],
-                                               gene_node_type])
+                                               gene_node_type,
+                                               str(is_tclin),
+                                               str(is_tchem)])
 
                     # WRITE EDGES
                     # ['subject', 'edge_label', 'object', 'relation', 'provided_by',
@@ -104,6 +123,42 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
         return None
 
 
+def tsv_to_dict(input_file: str, col_for_key: str) -> dict:
+    this_dict: dict = defaultdict(list)
+    with open(input_file) as file:
+        reader = csv.DictReader(file, delimiter='\t')
+        for row in reader:
+            this_dict[row[col_for_key]] = row
+    return this_dict
+
+
+def unzip_and_get_tclin_tchem(zip_file: str, output_dir: str) -> List[str]:
+    unzip_to_tempdir(zip_file, output_dir)
+    # get tclin filename
+    tclin_files = \
+        [f for f in os.listdir(output_dir) if re.match(r'tclin_.*\.tsv', f)]
+    if len(tclin_files) > 1:
+        raise RuntimeError("Found more than one tclin file:\n%s" %
+                           "\n".join(tclin_files))
+    elif len(tclin_files) < 1:
+        raise RuntimeError("Couldn't find tclin file in zipfile %s" % zip_file)
+    else:
+        tclin_file: str = os.path.join(output_dir, tclin_files[0])
+
+    # get tchem filename
+    tchem_files = \
+        [f for f in os.listdir(output_dir) if re.match(r'tchem_.*\.tsv', f)]
+    if len(tchem_files) > 1:
+        raise RuntimeError("Found more than one tchem file:\n%s" %
+                           "\n".join(tchem_files))
+    elif len(tchem_files) < 1:
+        raise RuntimeError("Couldn't find tchem file in zipfile %s" % zip_file)
+    else:
+        tchem_file: str = os.path.join(output_dir, tchem_files[0])
+
+    return [tclin_file, tchem_file]
+
+
 def parse_drug_central_line(this_line: str, header_items: List) -> Dict:
     """Methods processes a line of text from Drug Central.
 

tests/resources/drug_central/tchem_SNIPPET.tsv

@@ -0,0 +1,3 @@
+uniprot	swissprot	drug_name	act_value	act_type	action_type	source_name	reference	smiles	ChEMBL_Id
+P42338	PK3CB_HUMAN	copanlisib	8.431797981262207	IC50	INHIBITOR	SCIENTIFIC LITERATURE	http://www.ncbi.nlm.nih.gov/pubmed/24170767	COC1=C(OCCCN2CCOCC2)C=CC2=C1N=C(NC(=O)C1=CN=C(N)N=C1)N1CCN=C21	CHEMBL3218576
+P21917	DRD4_HUMAN	brexpiprazole	8.200659451	Ki	AGONIST	SCIENTIFIC LITERATURE	http://www.ncbi.nlm.nih.gov/pubmed/24947465	O=C1NC2=C(C=C1)C=CC(OCCCCN1CCN(CC1)C1=C3C=CSC3=CC=C1)=C2	CHEMBL2105760

tests/resources/drug_central/tclin_SNIPPET.tsv

@@ -0,0 +1,3 @@
+uniprot	swissprot	drug_name	act_value	act_type	action_type	source_name	reference	smiles	ChEMBL_Id
+P19838	NFKB1_HUMAN	cepharanthine			INHIBITOR	SCIENTIFIC LITERATURE	http://www.ncbi.nlm.nih.gov/pubmed/31132753	[H][C@]12CC3=CC(OC4=CC=C(C[C@@H]5N(C)CCC6=CC7=C(OCO7)C(OC7=C(OC)C=C(CCN1C)C2=C7)=C56)C=C4)=C(OC)C=C3	CHEMBL449782
+Q13131	AAPK1_HUMAN	cepharanthine			INHIBITOR	SCIENTIFIC LITERATURE	http://www.ncbi.nlm.nih.gov/pubmed/31132753	[H][C@]12CC3=CC(OC4=CC=C(C[C@@H]5N(C)CCC6=CC7=C(OCO7)C(OC7=C(OC)C=C(CCN1C)C2=C7)=C56)C=C4)=C(OC)C=C3	CHEMBL449782

tests/test_drug_central.py

@@ -1,15 +1,18 @@
+import os
+import tempfile
 import unittest
 
 from kg_covid_19.transform_utils.drug_central.drug_central import \
-    parse_drug_central_line
+    parse_drug_central_line, unzip_and_get_tclin_tchem, tsv_to_dict
 from kg_covid_19.utils.transform_utils import parse_header
 from parameterized import parameterized
 
 
 class TestDrugCentral(unittest.TestCase):
 
     def setUp(self) -> None:
-        self.dti_fh = open('tests/resources/drug.target.interaction_SNIPPET.tsv', 'rt')
+        self.dti_fh = open(
+            'tests/resources/drug_central/drug.target.interaction_SNIPPET.tsv', 'rt')
 
     @parameterized.expand([
      ('STRUCT_ID', '4'),
@@ -38,4 +41,25 @@ def test_parse_drug_central_line(self, key, value):
         self.assertTrue(key in parsed)
         self.assertEqual(value, parsed[key])
 
+    @parameterized.expand([
+    ('tclin', 'tests/resources/drug_central/tclin_SNIPPET.tsv', 2, 'Q13131', 'drug_name', 'cepharanthine'),
+    ('tchem', 'tests/resources/drug_central/tchem_SNIPPET.tsv', 2, 'P21917', 'drug_name', 'brexpiprazole'),
+    ])
+    def test_tsv_to_dict(self, name, file, expected_rows, test_key, sub_key, test_val) -> None:
+        ret_val = tsv_to_dict(file, 'uniprot')
+        self.assertTrue(isinstance(ret_val, dict))
+        self.assertEqual(len(ret_val), expected_rows)
+        self.assertTrue(isinstance(ret_val, dict))
+        self.assertTrue(test_key in ret_val)
+        self.assertTrue(sub_key in ret_val.get(test_key))
+        self.assertEqual(ret_val[test_key][sub_key], test_val)
+
+    def test_unzip_and_get_tclin_tchem(self) -> None:
+        zip_file = "tests/resources/drug_central/test.zip"
+        tempdir = tempfile.mkdtemp()
+        (tclin, tchem) = unzip_and_get_tclin_tchem(zip_file, tempdir)
+        self.assertTrue(isinstance(tclin, str))
+        self.assertTrue(isinstance(tchem, str))
+        self.assertEqual(tclin, os.path.join(tempdir, 'tclin_05122020.tsv'))
+        self.assertEqual(tchem, os.path.join(tempdir, 'tchem_drugs_05122020.tsv'))