Merge pull request #220 from SMD-Bioinformatics-Lund/jw/load-chromoso…

…me-lengths

Remove loading chr sizes from file

CHANGELOG.md

@@ -20,6 +20,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ### Fixed
  - Resolved all type errors from tsc
  - Initial type hints added to command and db modules
+ - Remove unused file argument for load chromomsome info CLI command
  - Fixed various issues raised by pylint
 
 ## 3.0.1

gens/commands/load.py

@@ -210,13 +210,6 @@ def transcripts(file: TextIO, mane: TextIO, genome_build: GenomeBuild):
 
 
 @load.command()
-# FIXME: Remove? Does not seem to be used?
-@click.option(
-    "-f",
-    "--file",
-    type=click.File(),
-    help="Chromosome sizes in tsv format",
-)
 @click.option(
     "-b",
     "--genome-build",
@@ -232,7 +225,7 @@ def transcripts(file: TextIO, mane: TextIO, genome_build: GenomeBuild):
     help="Timeout for queries.",
 )
 @with_appcontext
-def chromosome_info(file: TextIO, genome_build: GenomeBuild, timeout: int):
+def chromosome_info(genome_build: GenomeBuild, timeout: int):
     """Load chromosome size information into the database."""
     db = app.config["GENS_DB"]
     # if collection is not indexed, create index
@@ -254,6 +247,7 @@ def chromosome_info(file: TextIO, genome_build: GenomeBuild, timeout: int):
         chromosomes_data = build_chromosomes_obj(chrom_data, genome_build, timeout)
     except Exception as err:
         raise click.UsageError(str(err))
+
     # remove old entries
     res = db[CHROMSIZES_COLLECTION].delete_many({"genome_build": int(genome_build)})
     LOG.info(