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Adjust logging and fix unwanted progress bar #296

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merged 2 commits into from
Oct 29, 2024
Merged

Adjust logging and fix unwanted progress bar #296

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ac13ec7
add missing disable bar flag in fast projection
JeanMainguy Oct 29, 2024
af0c675
use debug to inform on missing translation table in input files
JeanMainguy Oct 29, 2024
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2 changes: 1 addition & 1 deletion ppanggolin/annotate/annotate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -823,7 +823,7 @@ def read_org_gbff(
contig.add_metadata(Metadata(source="annotation_file", **metadata_dict))

if used_transl_table_arg:
logging.getLogger("PPanGGOLiN").info(
logging.getLogger("PPanGGOLiN").debug(
f"transl_table tag was not found for {used_transl_table_arg} CDS "
f"in {gbff_file_path}. Provided translation_table argument value was used instead: {translation_table}."
)
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1 change: 1 addition & 0 deletions ppanggolin/projection/projection.py
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Expand Up @@ -795,6 +795,7 @@ def annotate_input_genes_with_pangenome_families(
identity=identity,
coverage=coverage,
translation_table=translation_table,
disable_bar=disable_bar,
)
else:
_, seqid_to_gene_family = get_input_seq_to_family_with_all(
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