From 17d6c871a68c36c2481e0c8391a86804dde9abe1 Mon Sep 17 00:00:00 2001
From: Sara <sara.schulte@uni-duesseldorf.de>
Date: Mon, 27 Mar 2023 17:53:20 +0200
Subject: [PATCH] Add new parameter and optional included peptides
---
HOGVAX/hogvax.py | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
diff --git a/HOGVAX/hogvax.py b/HOGVAX/hogvax.py
index 7b32671..fc8e613 100644
--- a/HOGVAX/hogvax.py
+++ b/HOGVAX/hogvax.py
@@ -28,8 +28,12 @@ def get_parser():
help='If provided, binding affinities are converted to binary data.')
parser.add_argument('--binding-affinities', '-ba', dest='ba_matrix', required=True, type=str,
help='Binding affinity file for input peptides and alleles.')
+ parser.add_argument('--required_epitopes', '-epi', dest='required_epitopes',
+ help='File of peptides you want to be present in vaccine')
parser.add_argument('--min-hits', '-mh', dest='min_hits', default=1, type=int,
help='Minimum number of hits for an allele to be covered')
+ parser.add_argument('--maximize-peptides', dest='maximize_peptides', default=False,
+ help='Maximize number of peptides in the vaccine in a second optimization')
parser.add_argument('--embedding-length', default=0, type=int, help='Set length of embedding if used')
parser.add_argument('--embedded-peptides', type=str, help='File containing embedded peptides')
parser.add_argument('--embedded-epitope_features', type=str, help='Path to embedded epitope features')
@@ -70,8 +74,13 @@ def main():
peptides = read_peptides(args.peptides)
pep_count = len(peptides)
+ required_peptides = []
+ if args.required_epitopes:
+ print('Reading required epitopes')
+ required_peptides = read_peptides(args.required_epitopes)
+
drawing_enabled = False
- if pep_count <= 30:
+ if pep_count < 30:
print('Number of peptides below 30 -> drawing enabled')
drawing_enabled = True
@@ -100,9 +109,7 @@ def main():
leaves_dict, hog = linear_time_hog.compute_hog(str(pep_count), peptides, args.outdir, drawing_enabled)
print('Binarize ba predictions')
- if args.ba_threshold:
- print(args.ba_threshold)
- bin_matrix = binarize_entries(mod_ba_df, args.ba_threshold)
+ bin_matrix = binarize_entries(mod_ba_df, args.ba_threshold)
full_known_alleles = gp.tuplelist(key for key in f_data.keys() if key in bin_matrix.keys())
@@ -117,6 +124,8 @@ def main():
min_hits=args.min_hits,
populations=args.populations,
path=args.outdir,
+ optional_peptides=required_peptides,
+ maximize_peptides=args.maximize_peptides,
logging=args.logging_enabled,
coloring=drawing_enabled)
--
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