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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2024-08-07 11:41:02 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2024-08-07 11:41:02 +0800 |
| commit | 4b64732ce6acdf75cf5b8469e42f15e625fee8b0 (patch) | |
| tree | 2fe4af167e26a040f5fed8ec2896522e49a426f4 | |
| parent | 173161a747ab2abb4a0d2a7dddecb39ddc9a4589 (diff) | |
Important files and directories
| -rw-r--r-- | Code/configure.py | 2 | ||||
| -rw-r--r-- | Code/merge_edges.py | 11 |
2 files changed, 6 insertions, 7 deletions
diff --git a/Code/configure.py b/Code/configure.py index 1ac9691..4ce159a 100644 --- a/Code/configure.py +++ b/Code/configure.py @@ -50,7 +50,7 @@ MAPPED_CDATA_DIR = '../Data/C/Mapped' # mapped ChIp-seq data # Used in merge_edges.py
EDGE_POOL_DIR = '/disk1/edge_pool'
MERGED_EDGE_FILE = '../Data/temp/edges.txt'
-
+SQLITE_EDGE_FILE = '../Data/temp/edges.sqlite'
DIFF_EDGE_FILE = '../Data/temp/edges-diff.txt' # the difference between two edge files from yesterday and from today
TARGET_TF_FILE = '../Data/information/target_tf.txt'
diff --git a/Code/merge_edges.py b/Code/merge_edges.py index 780da95..6bbd2f0 100644 --- a/Code/merge_edges.py +++ b/Code/merge_edges.py @@ -22,7 +22,7 @@ import os, operator, sys, math, datetime, glob from log import write_log_file -from configure import EDGE_POOL_DIR, MERGED_EDGE_FILE, UPDATE_NETWORK_LOG_FILE +from configure import EDGE_POOL_DIR, MERGED_EDGE_FILE, SQLITE_EDGE_FILE, UPDATE_NETWORK_LOG_FILE import sqlite3 def get_number_of_RNAseq_ids(s): @@ -210,13 +210,12 @@ fout.close() # Write edge information to SQLite database file, which could be opened using software called "DB Browser for SQLite" # Biologists may use this file for filtering the information they need. -db_fname = os.path.join(folder_path, 'edges.sqlite') -write_log_file('[merge_edges.py] Make SQLite database file %s.' % (db_fname), UPDATE_NETWORK_LOG_FILE) +write_log_file('[merge_edges.py] Make SQLite database file %s.' % (SQLITE_EDGE_FILE), UPDATE_NETWORK_LOG_FILE) -if os.path.exists(db_fname): - os.remove(db_fname) +if os.path.exists(SQLITE_EDGE_FILE): + os.remove(SQLITE_EDGE_FILE) -conn = sqlite3.connect(db_fname) +conn = sqlite3.connect(SQLITE_EDGE_FILE) c = conn.cursor() c.execute('CREATE TABLE IF NOT EXISTS edge (target_id text, target_name text, tf_id text, tf_name text, strength text, date text, method text, evidence text)') for k in d: |