Merge pull request #51 from Clinical-Genomics/rename_function

Rename fetch_ensembl_exon_lines function to fetch_ensembl_exons

CHANGELOG.md

@@ -5,6 +5,7 @@
 - Typo in instructions to download genes in README document
 ### Changed
 - Code formatted with black and black check GitHub action
+- Renamed `schug.load.ensembl.fetch_ensembl_exon_lines` function to `schug.load.ensembl.fetch_ensembl_exons`
 
 ## [1.2]
 ### Added

schug/cli/fetch.py

@@ -3,7 +3,6 @@
 import typer
 from schug.load.biomart import EnsemblBiomartClient
 from schug.load.ensembl import (
-    fetch_ensembl_exon_lines,
     fetch_ensembl_exons,
     fetch_ensembl_genes,
     fetch_ensembl_transcripts,
@@ -42,7 +41,7 @@ def ensembl_transcripts(build: str = typer.Option("37", "-b", "--build")):
 @app.command()
 def ensembl_exons(build: str = typer.Option("37", "-b", "--build")):
     """Fetch genes from ensembl"""
-    ensembl_client: EnsemblBiomartClient = fetch_ensembl_exon_lines(
+    ensembl_client: EnsemblBiomartClient = fetch_ensembl_exons(
         build=build, chromosomes=["Y"]
     )
     for line in ensembl_client:

schug/cli/load.py

@@ -5,7 +5,7 @@
 from pydantic import parse_obj_as
 from schug.database.genes import create_gene_item
 from schug.load.ensembl import (
-    fetch_ensembl_exon_lines,
+    fetch_ensembl_exons,
     fetch_ensembl_genes,
     fetch_ensembl_transcripts,
 )
@@ -24,7 +24,7 @@ def exons(
     """Load exon data"""
     typer.echo("Loading exons")
     if not exons_file:
-        exons_file = fetch_ensembl_exon_lines(build=build, chromosomes=["Y"])
+        exons_file = fetch_ensembl_exons(build=build, chromosomes=["Y"])
     parsed_exons = parse_obj_as(
         List[EnsemblExon],
         [parsed_line for parsed_line in csv.DictReader(exons_file, delimiter="\t")],

schug/endpoints/exons.py

@@ -3,7 +3,7 @@
 from fastapi import APIRouter, Depends, HTTPException, Query, status
 from fastapi.responses import StreamingResponse
 from schug.database.session import get_session
-from schug.load.ensembl import fetch_ensembl_exon_lines
+from schug.load.ensembl import fetch_ensembl_exons
 from schug.load.fetch_resource import stream_resource
 from schug.models import Exon, ExonRead
 from schug.models.common import Build
@@ -27,7 +27,7 @@ def read_exons(
 async def ensembl_exons(build: Build):
     """A proxy to the Ensembl Biomart that retrieves exons in a specific genome build."""
 
-    ensembl_client: EnsemblBiomartClient = fetch_ensembl_exon_lines(build=build)
+    ensembl_client: EnsemblBiomartClient = fetch_ensembl_exons(build=build)
     url: str = ensembl_client.build_url(xml=ensembl_client.xml)
 
     return StreamingResponse(stream_resource(url), media_type="text/tsv")

schug/load/ensembl.py

@@ -84,10 +84,10 @@ def fetch_ensembl_transcripts(
     return fetch_ensembl_biomart(attributes=attributes, filters=filters, build=build)
 
 
-def fetch_ensembl_exon_lines(
+def fetch_ensembl_exons(
     build: str, chromosomes: Optional[List[str]] = None
 ) -> EnsemblBiomartClient:
-    """Fetch the ensembl exons"""
+    """Fetch the ensembl exons."""
     chromosomes = chromosomes or CHROMOSOMES
     LOG.info("Fetching ensembl exons")
 
@@ -109,18 +109,3 @@ def fetch_ensembl_exon_lines(
     filters = {"chromosome_name": chromosomes}
 
     return fetch_ensembl_biomart(attributes=attributes, filters=filters, build=build)
-
-
-def fetch_ensembl_exons(
-    build: str, chromosomes: Optional[List[str]] = None
-) -> List[EnsemblExon]:
-    """Fetch ensembl exon objects"""
-    exon_lines: EnsemblBiomartClient = fetch_ensembl_exon_lines(
-        build=build, chromosomes=chromosomes
-    )
-
-    parsed_exons = parse_obj_as(
-        List[EnsemblExon],
-        [exon_info for exon_info in csv.DictReader(exon_lines, delimiter="\t")],
-    )
-    return parsed_exons