diff --git a/docs/generate_class1_pan.py b/docs/generate_class1_pan.py index dff0406921fd6be6bd8438edc28e227bfe461df5..785ecc3dd8682b1f23404ccade430234093ab9c7 100644 --- a/docs/generate_class1_pan.py +++ b/docs/generate_class1_pan.py @@ -22,9 +22,10 @@ AMINO_ACIDS = sorted(COMMON_AMINO_ACIDS) parser = argparse.ArgumentParser(usage=__doc__) parser.add_argument( "--class1-models-dir-with-ms", + "--class1-models", metavar="DIR", default=get_path( - "models_class1_pan", "models.with_mass_spec", test_exists=False), + "models_class1_pan", "models.combined", test_exists=False), help="Class1 models. Default: %(default)s", ) parser.add_argument( @@ -190,9 +191,7 @@ def go(argv): mkdir(args.out_dir) predictors = [ - ("with_mass_spec", args.class1_models_dir_with_ms), - ("refined", args.class1_models_dir_refined), - ("no_mass_spec", args.class1_models_dir_no_ms), + ("combined", args.class1_models_dir_with_ms), ] info_per_predictor = OrderedDict() alleles = set() @@ -250,11 +249,7 @@ def go(argv): models_label=label) if not length_distribution_image_path: continue - w("*%s*\n" % { - "with_mass_spec": "With mass-spec", - "no_mass_spec": "Affinities only", - "refined": "With mass-spec after multiallelic refinement", - }[label]) + w("*%s*\n") if info['observations_per_allele'] is not None: w("Training observations (unique peptides): %d" % ( info['observations_per_allele'].get(allele, 0))) diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml index 9598be02d2b2414751e4e63cbd9a087b8d9f176a..0074942d5946f02ea6a2a92cfc5e60fbce0ab243 100644 --- a/mhcflurry/downloads.yml +++ b/mhcflurry/downloads.yml @@ -33,7 +33,7 @@ releases: default: false - name: models_class1_pan_variants - url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan_variants.selected.20200103.tar.bz2 + url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan_variants.selected.20200106.tar.bz2 default: false - name: data_mass_spec_benchmark