From 5e17f211bd2482a414625eb25c3d3a7dc40bf1b8 Mon Sep 17 00:00:00 2001
From: Sara <sara.schulte@uni-duesseldorf.de>
Date: Thu, 13 Apr 2023 19:22:08 +0200
Subject: [PATCH] Remove output for debugging purpose and update ilp
---
HOGVAX/hogvax_ilp.py | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/HOGVAX/hogvax_ilp.py b/HOGVAX/hogvax_ilp.py
index e483d83..9c79ddd 100644
--- a/HOGVAX/hogvax_ilp.py
+++ b/HOGVAX/hogvax_ilp.py
@@ -116,9 +116,9 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
log('Add allele hit constraint')
for allele in alleles:
# check for peptides (leaf nodes) with non-zero entry in B matrix for current allele
- hit_leaves = list(filter(lambda x: 1.0 == B_matrix[allele][x], leaves.keys()))
+ hit_pep = list(filter(lambda x: 1.0 == B_matrix[allele][x], leaves.keys()))
# only sum over such peptides instead of summing over all peptides -> only beneficial for ba threshold > 0.xx
- m.addConstr(hit[allele] * min_hits <= gp.quicksum(x_edges.sum('*', leaves[leaf]) for leaf in hit_leaves),
+ m.addConstr(hit[allele] * min_hits <= gp.quicksum(x_nodes[leaves[pep]] for pep in hit_pep),
'Peptide-hit for allele ' + '_'.join(allele))
m.update()
@@ -163,10 +163,11 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
if node_b in leaves.values():
chosen_pep.append(graph.nodes[node_b]['string'])
- if not os.path.exists(path + 'lp_out/'):
- os.mkdir(path + 'lp_out/')
- m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.sol')
- m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.json')
+ # also only for more details and debugging
+ # if not os.path.exists(path + 'lp_out/'):
+ # os.mkdir(path + 'lp_out/')
+ # m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.sol')
+ # m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.json')
if not os.path.exists(path + 'pep_out/'):
os.mkdir(path + 'pep_out/')
@@ -214,6 +215,7 @@ def hogvax(k, alleles, freq_vector, B_matrix, leaves, pep_count, graph, path, mi
if node_inner in subtour and node_outer not in subtour),
'At least one incoming edge to subtour ' + str(i) + ' from the outside')
- m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.lp')
+ # only for debugging, lp file becomes quite large
+ # m.write(path + 'lp_out/' + pep_count + '_vaccine_ilp_hog.lp')
return chosen_pep
--
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