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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2020-02-14 17:27:31 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2020-02-14 17:28:24 +0800 |
| commit | a172ac560fd3c8b11f0ab1370bd015203c134de9 (patch) | |
| tree | f198b8802798bae1b60d392957a67a14a5233b5b | |
| parent | 86a521351b4834cb9e00e0979e84cb3ffedfda55 (diff) | |
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.
| -rw-r--r-- | Code/merge_edges.py | 4 |
1 files changed, 3 insertions, 1 deletions
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: |