Skip to content

Commit

Permalink
Improve arg help desc
Browse files Browse the repository at this point in the history
  • Loading branch information
lauraluebbert authored Oct 21, 2024
1 parent b81030f commit 13db831
Showing 1 changed file with 7 additions and 5 deletions.
12 changes: 7 additions & 5 deletions gget/gget_ncbi_virus.py
Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ def filter_sequences(
max_protein_count=None,
max_ambiguous_chars=None,
has_proteins=None,
proteins_complete=None,
proteins_complete=False,
):
"""Filter sequences based on various metadata criteria."""

Expand Down Expand Up @@ -552,7 +552,7 @@ def ncbi_virus(
max_gene_count=None,
nuc_completeness=None,
has_proteins=None,
proteins_complete=None,
proteins_complete=False,
host_taxid=None,
lab_passaged=None,
geographic_region=None,
Expand All @@ -577,7 +577,8 @@ def ncbi_virus(
- virus Virus taxon or accession, e.g. 'Norovirus' or 'coronaviridae' or
'11320' (taxid of Influenza A virus) or 'NC_045512.2'
If this input is a virus NCBI accession (e.g. 'NC_045512.2'), set accession = True.
- accession True/False whether 'virus' is an accession. Default: False
- accession Set to True when argument 'virus' is an NCBI accession (NCBI accessions begin with 'NC').
Default: False
- outfolder Path to folder to save the requested data in, e.g. 'path/to/norovirus_folder'.
Default: None (saves output into current working directory)
Expand All @@ -591,7 +592,8 @@ def ncbi_virus(
- has_proteins Str or list of proteins, genes, or segments that should be present in the sequence
(based on sequence annotation provided by the submitter). Default: None
Note: Set proteins_complete=True to only include sequences for which the proteins/genes/segments are marked 'complete'
- proteins_complete Set to True if proteins/genes/segments in has_proteins should be marked as complete. Default: False
- proteins_complete Set to True if proteins/genes/segments in has_proteins should be marked as complete.
Default: False (returns all sequences regardless of whether the proteins in has_proteins are marked as complete)
- host_taxid NCBI Taxonomy ID of the host organism. Filters the results to only include viruses
associated with hosts that fall within the specified TaxID. Default: None
- lab_passaged True/False Indicates whether the virus sequence has been passaged in a laboratory setting.
Expand Down Expand Up @@ -640,7 +642,7 @@ def ncbi_virus(
)
if proteins_complete is not None and not isinstance(proteins_complete, bool):
raise TypeError(
"Argument 'proteins_complete' must be a boolean (True or False) or None."
"Argument 'proteins_complete' must be a boolean (True or False)."
)
if isinstance(virus, int):
virus = str(virus)
Expand Down

0 comments on commit 13db831

Please sign in to comment.