Merge a3a27c8 into b630715

kg_covid_19/query.py

@@ -0,0 +1,14 @@
+import logging
+
+from kg_covid_19.query_utils.target_candidates.target_candidates \
+    import TargetCandidates
+
+QUERIES = {
+    'TargetCandidates': TargetCandidates
+}
+
+
+def run_query(query: str, input_dir: str, output_dir: str) -> None:
+    logging.info(f"Running query {query}")
+    t = QUERIES[query](input_dir, output_dir)
+    t.run()

kg_covid_19/query_utils/query.py

@@ -0,0 +1,8 @@
+class Query:
+    def __init__(self, query_name: str, input_dir: str, output_dir: str) -> None:
+        self.query_name = query_name
+        self.input_dir = input_dir
+        self.output_dir = output_dir
+
+    def run(self, input_dir: str, output_dir: str) -> None:
+        pass

kg_covid_19/query_utils/target_candidates/target_candidates.py

@@ -0,0 +1,277 @@
+import csv
+import logging
+import os
+import re
+import tarfile
+from typing import List, Union
+
+from tqdm import tqdm  # type: ignore
+
+from kg_covid_19.query_utils.query import Query
+import pandas as pd  # type: ignore
+
+
+class TargetCandidates(Query):
+    """Perform a query of TSV files to generate a short list of protein targets
+    for further investigation.
+
+    A tsv file is emitted with these fields:
+    species H=host, V=viral
+    protein ID
+    protein/gene name
+    confidence score 0-1
+    Free text describing why target was chosen
+
+    This software is provided "as is" and any expressed or implied warranties,
+    including, but not limited to, the implied warranties of merchantability and
+    fitness for a particular purpose are disclaimed. in no event shall the authors or
+    contributors be liable for any direct, indirect, incidental, special, exemplary, or
+    consequential damages (including, but not limited to, procurement of substitute
+    goods or services; loss of use, data, or profits; or business interruption)
+    however caused and on any theory of liability, whether in contract, strict
+    liability, or tort (including negligence or otherwise) arising in any way out of
+    the use of this software, even if advised of the possibility of such damage.
+    """
+
+    def __init__(self, input_dir: str, output_dir: str):
+        query_name = "target_candidates"
+        super().__init__(query_name, input_dir, output_dir)  # set some variables
+        # data file locations
+        self.intact_nodes_file = os.path.join('transformed', 'intact', 'nodes.tsv')
+        self.intact_edges_file = os.path.join('transformed', 'intact', 'edges.tsv')
+        self.sars_cov_2_nodes = os.path.join('data', "transformed",
+                                             "sars_cov_2_gene_annot/nodes.tsv")
+        self.sars_cov_2_edges = os.path.join('data', "transformed",
+                                             "sars_cov_2_gene_annot/edges.tsv")
+        self.outfile_name = "target_candidates.tsv"
+        self.outfile_header = ["species",
+                               "protein ID",
+                               "protein/gene name",
+                               "confidence score",
+                               "comments"]
+
+    def run(self):
+        candidates: list = []
+
+        # read in data files
+        logging.info("reading in data files")
+        sars_cov2_df = pd.read_csv(self.sars_cov_2_nodes, sep="\t")
+        intact_edges_df = pd.read_csv(os.path.join(self.input_dir,
+                                                   self.intact_edges_file),
+                                      sep='\t')
+        intact_nodes_df = pd.read_csv(os.path.join(self.input_dir,
+                                                   self.intact_nodes_file),
+                                      sep='\t')
+
+        # add SARS-CoV-2 proteins from gene annotation transform
+        logging.info("adding annotated SARS-CoV-2 proteins from annotations")
+        candidates.extend(
+            self.sars_cov2_to_candidate_entries(sars_cov2_df,
+                                              'V', 'id', 'name', 1,
+                                              "annotated SARS-CoV-2 gene"))
+        sars_cov2_ids = [c[1] for c in candidates]
+
+        # append PRO_ SARS-CoV-2 proteins
+        logging.info("adding SARS-CoV-2 proteins PRO_ proteins")
+        candidates.extend(
+            self.sars_cov2_pro_candidates(sars_cov2_ids,
+                                          sars_cov2_df,
+                                          'V', 'id', 'name', 1,
+                                          "annotated SARS-CoV-2 gene"))
+
+        sars_cov2_ids_plus_pro = [c[1] for c in candidates]
+
+        logging.info("adding SARS-CoV-2 proteins present in IntAct")
+        candidates.extend(
+            self.sars_cov2_in_intact_set_to_candidate_entries(
+                                            existing_ids=sars_cov2_ids_plus_pro,
+                                            taxon_id=2697049,
+                                            nodes_df=intact_nodes_df,
+                                            taxid_col='ncbi_taxid')
+        )
+
+        all_sars_cov2_ids = [c[1] for c in candidates]
+
+        # append list of proteins that interact with SARS-CoV-2 according to IntAct
+        logging.info("adding human proteins that interact with SARS-CoV-2 proteins" +
+                     "according to IntAct")
+        candidates.extend(
+        self.sars_cov2_human_interactors_to_candidate_entries(
+                            sars_cov2_ids=all_sars_cov2_ids,
+                            provided_by='intact',
+                            edge_df=intact_edges_df,
+                            nodes_df=intact_nodes_df,
+                            viral_or_host="H",
+                            subject_and_object_columns=['subject', 'object'],
+                            id_col_in_node_tsv='id',
+                            name_col='name',
+                            confidence_score=0.75,
+                            comments='inferred from intact')
+        )
+
+        os.makedirs(self.output_dir, exist_ok=True)
+        with open(os.path.join(self.output_dir, self.outfile_name), 'w', newline="") as out:
+            tsv_output = csv.writer(out, delimiter='\t')
+            tsv_output.writerow(self.outfile_header)
+            for candidate in candidates:
+                tsv_output.writerow(candidate)
+
+    def sars_cov2_in_intact_set_to_candidate_entries(self,
+                                                     existing_ids: list,
+                                                     taxon_id: int,
+                                                     nodes_df,
+                                                     taxid_col: str,
+                                                     id_col = 'id',
+                                                     name_col = 'name'
+                                                     ):
+        """Extract list of SARS-CoV-2 protein from IntAct nodes file
+
+        :param taxid_col: column name with taxon id
+        :param existing_ids: exclude entries present in this list
+        :param taxon_id: taxon ID to search for
+        :param nodes_df: pandas dataframe for intact nodes
+        :return:
+        """
+
+        candidate_entries: list = []
+        rows = nodes_df[nodes_df[taxid_col] == taxon_id]
+        for _, row in rows.iterrows():
+            if row[id_col] not in existing_ids:
+                candidate_entries.append(['V', row[id_col], row[name_col], 1,
+                                          'present in intact database'])
+        return candidate_entries
+
+    def sars_cov2_pro_candidates(self,
+                                 these_ids: list,
+                                 sars_cov2_df,
+                                 viral_or_host: str,
+                                 id_col: str,
+                                 name_col: str,
+                                 confidence_score: str,
+                                 comments: str):
+        """Given sars-cov-2 gene annotations, extract and make candidate entry
+        :param IDs for which to look in nodes df for PRO_ genes
+        :param sars_cov2_df:
+        :param viral_or_host:
+        :param id_col:
+        :param name_col:
+        :param confidence_score:
+        :param comments:
+
+        :return: List - candidate entry in format described in docstring
+        """
+        candidate_entries: list = []
+
+        all_ids = list(sars_cov2_df[id_col])
+        all_names = list(sars_cov2_df[name_col])
+        for id_to_match in these_ids:
+            this_re = re.compile(id_to_match)
+            matching_indices = [i for i, item in enumerate(all_ids) if this_re.search(item)]
+
+            for this_idx in matching_indices:
+                this_id = all_ids[this_idx]
+                this_name = all_names[this_idx]
+
+                if this_id == id_to_match:  # don't match identical IDs
+                    continue
+                candidate_entry = [viral_or_host, this_id, this_name, confidence_score, comments]
+                candidate_entries.append(candidate_entry)
+        return candidate_entries
+
+    def sars_cov2_to_candidate_entries(self,
+                                       sars_cov2_df,
+                                       viral_or_host: str,
+                                       id_col: str,
+                                       name_col: str,
+                                       confidence_score: str,
+                                       comments: str
+                                       ) -> List[List[Union[str, int]]]:
+        """Given sars-cov-2 gene annotations, extract and make candidate entry
+
+        :param comments:
+        :param confidence_score:
+        :param name_col:
+        :param id_col:
+        :param viral_or_host:
+        :param sars_cov2_df:
+        :return: List - candidate entry in format described in docstring
+        """
+        candidate_entries: list = []
+
+        for _, row in sars_cov2_df.iterrows():
+            candidate_entry = [viral_or_host, None, None, confidence_score, comments]
+            if id_col in row:
+                candidate_entry[1] = row[id_col]
+            if name_col in row:
+                candidate_entry[2] = row[name_col]
+            candidate_entries.append(candidate_entry)
+        return candidate_entries
+
+    def sars_cov2_human_interactors_to_candidate_entries(self,
+                                                         sars_cov2_ids: list,
+                                                         provided_by: str,
+                                                         edge_df,
+                                                         nodes_df,
+                                                         viral_or_host: str,
+                                                         subject_and_object_columns: list,
+                                                         id_col_in_node_tsv: str,
+                                                         name_col: str,
+                                                         confidence_score: float,
+                                                         comments: str
+                                                         ) -> List[List[Union[str, int]]]:
+        """Given sars-cov-2 genes and a pandas DF with edge data and node data, extract
+        all proteins that interact with these sars-cov2 genes according to source(s) in
+        'provided_by'
+
+        :param id_cols:
+        :param nodes_df:
+        :param sars_cov2_ids
+        :param provided_by
+        :param edge_df
+        :param node_df
+        :param viral_or_host:
+        :param id_col:
+        :param edge_df,
+        :param comments:
+        :param confidence_score:
+        :param name_col:
+        :param sars_cov2_df:
+        :return: List - candidate entry in format described in docstring
+        """
+        candidate_entries: list = []
+
+        # find edges for 'provided_by'
+        these_edges = edge_df[edge_df.provided_by == provided_by]
+
+        interactor_ids: list = []
+
+        # find IDs of interest in id_cols_to_search
+        for this_id in tqdm(sars_cov2_ids):
+
+            for _, row in these_edges.iterrows():
+                if row[subject_and_object_columns[0]] == this_id:
+                    interactor_col_name = subject_and_object_columns[1]
+                elif row[subject_and_object_columns[1]] == this_id:
+                    interactor_col_name = subject_and_object_columns[0]
+                else:
+                    continue
+
+                interactor_ids.append(row[interactor_col_name])
+
+        interactor_ids = list(set(interactor_ids))
+
+        for interactor_id in interactor_ids:
+            # find interactor name
+            name = "NA"
+            try:
+                node_rows = nodes_df[nodes_df[id_col_in_node_tsv] == interactor_id]
+                name = node_rows[name_col][0]
+            except KeyError:
+                logging.warning("Problem getting name for id: %s", interactor_id)
+                pass
+
+            candidate_entry = [viral_or_host, interactor_id, name, confidence_score,
+                               comments]
+            candidate_entries.append(candidate_entry)
+
+        return candidate_entries

kg_covid_19/transform_utils/intact/intact.py

@@ -51,6 +51,7 @@ def __init__(self, input_dir: str = None, output_dir: str = None) -> None:
         self.pubmed_curie_prefix = 'PMID:'
         self.ppi_edge_label = 'biolink:interacts_with'
         self.ppi_ro_relation = 'RO:0002437'
+        self.node_header = ['id', 'name', 'category', 'ncbi_taxid']
         self.edge_header = ['subject', 'edge_label', 'object', 'relation', 'provided_by',
                             'publication', 'num_participants', 'association_type',
                             'detection_method',  'subj_exp_role', 'obj_exp_role']
@@ -233,6 +234,12 @@ def interactor_to_node(self, interactor) -> List[Union[int, list]]:
                 "Problem parsing id in xref interaction %s" % e)
 
         name = ''
+
+        try:
+            tax_id = interactor.getElementsByTagName('organism')[0].attributes['ncbiTaxId'].value
+        except (KeyError, IndexError, AttributeError) as e:
+            tax_id = "NA"
+
         try:
             # xml parsing amirite
             name = interactor.getElementsByTagName('names')[0].getElementsByTagName(
@@ -253,7 +260,7 @@ def interactor_to_node(self, interactor) -> List[Union[int, list]]:
             logging.warning(
                 "Problem parsing name in xref interaction %s" % e)
 
-        return [interactor_id, [this_id, name, category]]
+        return [interactor_id, [this_id, name, category, tax_id]]
 
     def parse_experiment_info(self, xmldoc: object) -> Dict[int, str]:
         """Extract info about experiment from miXML doc

run.py

@@ -1,20 +1,23 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
+import logging
 
 import click
 from kg_covid_19 import download as kg_download
 from kg_covid_19 import transform as kg_transform
 from kg_covid_19.load_utils.merge_kg import load_and_merge
+from kg_covid_19.query import QUERIES, run_query
 from kg_covid_19.transform import DATA_SOURCES
 
+
 @click.group()
 def cli():
     pass
 
 
 @cli.command()
-@click.option("yaml_file", "-y", required=True, default="download.yaml", type=click.Path(exists=True))
+@click.option("yaml_file", "-y", required=True, default="download.yaml",
+              type=click.Path(exists=True))
 @click.option("output_dir", "-o", required=True, default="data/raw")
 @click.option("ignore_cache", "-i", is_flag=True, default=False,
               help='ignore cache and download files even if they exist [false]')
@@ -40,7 +43,8 @@ def download(*args, **kwargs) -> None:
 @cli.command()
 @click.option("input_dir", "-i", default="data/raw", type=click.Path(exists=True))
 @click.option("output_dir", "-o", default="data/transformed")
-@click.option("sources", "-s", default=None, multiple=True, type=click.Choice(DATA_SOURCES.keys()))
+@click.option("sources", "-s", default=None, multiple=True,
+              type=click.Choice(DATA_SOURCES.keys()))
 def transform(*args, **kwargs) -> None:
     """Calls scripts in kg_covid_19/transform/[source name]/ to transform each source
     into nodes and edges.
@@ -77,5 +81,26 @@ def load(yaml: str) -> None:
     load_and_merge(yaml)
 
 
+@cli.command()
+@click.option("query", "-q", required=True, default=None, multiple=False,
+              type=click.Choice(QUERIES.keys()))
+@click.option("input_dir", "-i", default="data/")
+@click.option("output_dir", "-o", default="data/queries/")
+def query(query: str, input_dir: str, output_dir: str) -> None:
+    """Perform a query of knowledge graph using a class contained in query_utils
+
+    Args:
+        query: A query class containing instructions for performing a query
+        input_dir: Directory where any input files required to execute query are
+        located (typically 'data', where transformed and merged graph files are)
+        output_dir: Directory to output results of query
+
+    Returns:
+        None.
+
+    """
+    run_query(query=query, input_dir=input_dir, output_dir=output_dir)
+
+
 if __name__ == "__main__":
     cli()