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Fix to Path declaration and docs string tweaks
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ens-LCampbell committed Apr 10, 2024
1 parent be90eed commit af6d341
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions src/python/ensembl/io/genomio/assembly/status.py
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def singularity_image_setter(sif_cache_dir: Path, datasets_version: str) -> Clie
container and define version and location of container.
Args:
sif_cache_dir: Path to attempt locating/download SIF container image.
sif_cache_dir: Path to locate existing, or download new SIF container image.
datasets_version: URL of singularity container (custom 'datasets' version if desired)
Returns:
Expand Down Expand Up @@ -121,10 +121,10 @@ def check_parameterization(input_cores: Path, input_accessions: Path, db_host: s
incorrect parameterization.
Args:
input_cores: input core(s) list file name.
input_accessions: input accession (s) list file name.
db_host: host server name
db_port: host server port
input_cores: Input core(s) list file name.
input_accessions: Input accession (s) list file name.
db_host: Host server name
db_port: Host server port
Returns:
User input file used in assembly status querying
Expand All @@ -149,8 +149,8 @@ def resolve_query_type(
Args:
query_list: List of user defined queries either core names, or accessions
partial_url: A partial MYSQL connection URL (host:port)
input_cores: arg parse param '--input_cores'
input_accessions: arg parse param '--input_accns'
input_cores: Arg parse param '--input_cores'
input_accessions: Arg parse param '--input_accessions'
Returns:
User queries stored as identifier[(core db name | UniqueID#)] : accession
Expand Down Expand Up @@ -258,7 +258,7 @@ def datasets_asm_reports(
batch_reports_json = tmp_asm_dict["reports"]
for assembly_report in batch_reports_json:
accession = assembly_report["accession"]
asm_json_outfile = Path(download_directory, f"/{accession}.asm_report.json")
asm_json_outfile = Path(download_directory, f"{accession}.asm_report.json")
print_json(asm_json_outfile, assembly_report)
# Save assembly report into master core<>report dict
for core, accession_core in assembly_accessions.items():
Expand Down

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