brain: add python and R code to local repository.

1 files changed, 55 insertions, 0 deletions

diff --git a/Code/exclude_edges.py b/Code/exclude_edges.py
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+++ b/Code/exclude_edges.py
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+# 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+# Purpose: Exclude the edge whose TF is in exclude_tf_list, since we want to hide unpublished data.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()