From 2fabd904aae874dc13e5482881d95fae249c0f56 Mon Sep 17 00:00:00 2001
From: Sara <sara.schulte@uni-duesseldorf.de>
Date: Sat, 7 Jan 2023 22:40:29 +0100
Subject: [PATCH] Add changes for multi edge traversal
---
HOGVAX/hogvax.py | 4 ++--
HOGVAX/hogvax_ilp.py | 17 ++++++++---------
2 files changed, 10 insertions(+), 11 deletions(-)
diff --git a/HOGVAX/hogvax.py b/HOGVAX/hogvax.py
index ba3ebcc..7b32671 100644
--- a/HOGVAX/hogvax.py
+++ b/HOGVAX/hogvax.py
@@ -24,7 +24,7 @@ def get_parser():
help='Preprocessed peptide file with every peptide in a new line.')
parser.add_argument('--allele-frequencies', '-af', dest='f_data', required=True, type=str,
help='(Normalized) allele frequency file.')
- parser.add_argument('--ba-threshold', '-t', dest='ba_threshold', type=float,
+ parser.add_argument('--ba-threshold', '-t', dest='ba_threshold', default=0.638, type=float,
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.')
@@ -60,7 +60,7 @@ def main():
args = get_parser().parse_args()
if args.outdir:
- if '/' not in args.outdir:
+ if not args.outdir.endswith('/'):
args.outdir = args.outdir + '/'
if not os.path.exists(args.outdir):
os.mkdir(args.outdir)
diff --git a/HOGVAX/hogvax_ilp.py b/HOGVAX/hogvax_ilp.py
index 16764e2..a663b7a 100644
--- a/HOGVAX/hogvax_ilp.py
+++ b/HOGVAX/hogvax_ilp.py
@@ -57,17 +57,13 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
# create new model
m = gp.Model('ivp_on_hog')
- # set time limit to 10 hours
- m.setParam('TimeLimit', 36000)
+ # set time limit to 48 hours
+ m.setParam('TimeLimit', 172800)
m.setParam('Seed', 42)
random.seed(42)
numpy.random.seed(42)
- m.setParam('PoolSearchMode', 2)
- m.setParam('PoolSolutions', 10000)
- m.setParam('PoolGap', 0.0)
if not os.path.exists(path + 'lp_out/'):
os.mkdir(path + 'lp_out/')
- m.setParam('SolFiles', path + 'lp_out/' + pep_count)
# create hit variables
log('Create hit variables')
@@ -79,7 +75,7 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
log('Create edge variables')
x_edges = gp.tupledict()
for node_a, node_b in sorted(graph.edges):
- x_edges[node_a, node_b] = m.addVar(vtype=GRB.BINARY,
+ x_edges[node_a, node_b] = m.addVar(vtype=GRB.INTEGER,
name=graph.nodes[node_a]['string'] + '_' + graph.nodes[node_b]['string'])
# the objective function is to maximize population coverage
@@ -133,7 +129,9 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
for edge in x_edges:
node_a, node_b = edge
# print('%s -> %s: %g' % (node_a, node_b, sol[node_a, node_b]))
- if sol[node_a, node_b] >= 0.5:
+ # variable tolerance of gurobi is 1e-5
+ traversals = round(sol[node_a, node_b])
+ for i in range(traversals):
solution_edges.append(edge)
if node_a in leaves.values():
chosen_pep.append(graph.nodes[node_a]['string'])
@@ -159,8 +157,9 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
file.write('\n'.join(chosen_pep))
# create subgraph from edges chosen by ILP in order to find eulerian path to construct vaccine sequence
+ # use multi graph here to add edges that are traversed more than once multiple times to the graph
log('Create vaccine sequence')
- sub_hog = nx.DiGraph()
+ sub_hog = nx.MultiDiGraph()
sub_hog.add_edges_from(solution_edges)
log('sub graph is eulerian' + str(nx.is_eulerian(sub_hog)))
if coloring:
--
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