From 97fdefab064f63642fa3ece05b807d29b459df31 Mon Sep 17 00:00:00 2001
From: Hui Lan <lanhui@zjnu.edu.cn>
Date: Wed, 4 Dec 2019 19:03:19 +0800
Subject: brain: add python and R code to local repository.

---
 Code/exclude_edges.py | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 Code/exclude_edges.py

(limited to 'Code/exclude_edges.py')

diff --git a/Code/exclude_edges.py b/Code/exclude_edges.py
new file mode 100644
index 0000000..1fb5f77
--- /dev/null
+++ b/Code/exclude_edges.py
@@ -0,0 +1,55 @@
+# Usage: python exclude_edges.py edges.txt
+#
+# Purpose: Exclude the edge whose TF is in exclude_tf_list, since we want to hide unpublished data.  Don't distinguish +/- edges.
+#          For a TF-Target pair, use the edge that has largest value of metric.  If correlation is negative, use its absolute value.
+#
+# Created by Hui on 5 Jan 2018
+
+import os, sys
+
+def remove_minus(s):
+    ''' Remove the minus sign in s  '''
+    index = s.find('-')
+    return s[index+1:]
+
+
+def neg2pos(s):
+    s = s.strip()
+    lst = s.split('\t')
+    x = float(lst[2])
+    if x < 0:
+        lst[2] = remove_minus(lst[2])
+    return '\t'.join(lst)
+
+
+def make_edge_dict(fname, exclude_lst):
+    d = {}
+    f = open(fname)
+    for line in f:
+        line = line.strip()
+        lst = line.split('\t')
+        tf_id = lst[1].split()[0]
+        if not tf_id in exclude_lst:
+            target_id = lst[0].split()[0]
+            metric = float(lst[8])        
+            k = tf_id + '.' + target_id
+            if not k in d:
+                d[k] = {}
+                d[k]['metric']  = metric
+                d[k]['line'] = neg2pos(line) # make the third field (correlation) positive if it is negative. Indicate influence, not activation/repression.
+            else:
+                if d[k]['metric'] < metric:
+                    d[k]['metric'] = metric
+                    d[k]['line'] = neg2pos(line)
+    f.close()
+    return d
+    
+
+# main
+exclude_tf_list = ['AT4G26840', 'AT3G18550']
+edge_file_name = sys.argv[1]
+d = make_edge_dict(edge_file_name, exclude_tf_list)
+f = open(edge_file_name, 'w') # this will make edge.txt empty
+for k in sorted(d.keys()):
+    f.write('%s\n' % d[k]['line'])
+f.close()
-- 
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