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change logging to reduce non-failing noise
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sierra-moxon committed Sep 13, 2024
1 parent cf0c393 commit 540d355
Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions bin/validate.py
Original file line number Diff line number Diff line change
Expand Up @@ -771,19 +771,20 @@ def produce(ctx, group, metadata_dir, gpad, gpad_gpi_output_version, ttl, target
click.echo(os.path.split(end_gaf)[0])
temp_output_gaf_path = os.path.join(os.path.split(end_gaf)[0], "{}_temp.gaf".format(dataset))
click.echo("temp_output_gaf_path: {}".format(temp_output_gaf_path))
click.echo("matching_gpi_path".format(gpi))
click.echo("matching_gpi_path: {}".format(gpi))

isoform_fixed_gaf = fix_pro_isoforms_in_gaf(end_gaf, gpi, ontology_graph, temp_output_gaf_path)
click.echo("isoform_fixed_gaf: ".format(isoform_fixed_gaf))
click.echo("isoform_fixed_gaf: {}".format(isoform_fixed_gaf))

final_output_gaf_path = os.path.join(os.path.split(end_gaf)[0], "{}.gaf".format(dataset))

click.echo("Rename the temporary isoform fixed file to the final GAF...")
os.rename(temp_output_gaf_path, final_output_gaf_path)
click.echo("final_output_gaf_path: ".format(final_output_gaf_path))
click.echo("final_output_gaf_path: {}".format(final_output_gaf_path))

click.echo("Producing final GPI after all GAF corrections...")
final_gpi = produce_gpi(dataset, absolute_target, final_output_gaf_path, ontology_graph, gpad_gpi_output_version)
click.echo("final_gpi: {}".format(final_gpi))

click.echo("Creating ttl files...")
make_ttls(dataset, final_output_gaf_path, products, ontology_graph)
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