From a172ac560fd3c8b11f0ab1370bd015203c134de9 Mon Sep 17 00:00:00 2001 From: Hui Lan Date: Fri, 14 Feb 2020 17:27:31 +0800 Subject: merge_edges.py: write edge file names to network.log When merging many big edge files, the computer may run out of memory. Save the edge files that have been considered thus far and figure out where merging stopped. --- Code/merge_edges.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Code/merge_edges.py b/Code/merge_edges.py index d07447a..a2da07f 100644 --- a/Code/merge_edges.py +++ b/Code/merge_edges.py @@ -151,14 +151,16 @@ def make_new_edge(lst_tuple): best_edge[9] = ','.join(sorted(list(set(method_or_tissue)))) # unique methods or tissues, in string format return best_edge - + ##main + d = {} # d will contain all edges computed so far, where the key is TargetGeneID_TFGeneID, and the value is a list of tuples. Each tuple is a historical edge. file_count = 0 for fname in sorted(glob.glob(os.path.join(EDGE_POOL_DIR, 'edges*.*'))): file_count += 1 print('[merge_edges.py]: including %s.' % (fname)) + write_log_file('[merge_edges.py] including file %s.' % (fname) , UPDATE_NETWORK_LOG_FILE) f = open(fname) for line in f: -- cgit v1.2.1