brain: add python and R code to local repository.

1 files changed, 39 insertions, 0 deletions

diff --git a/Code/make_target_tf_agris.py b/Code/make_target_tf_agris.py
new file mode 100644
index 0000000..c96c8fa
--- /dev/null
+++ b/Code/make_target_tf_agris.py
@@ -0,0 +1,39 @@
+# Make target_tf from AtRegNet.txt
+# Usage: python make_target_tf_agris.py > ../Data/information/target_tf_agris.txt
+
+fname = '../Data/information/AtRegNet.txt'
+
+sample_id = 'C0000000000001'
+
+f = open(fname)
+lines = f.readlines()
+f.close()
+
+d = {}
+count = 2
+duplicate = 0
+for line in lines[1:]:
+    line = line.strip()
+    lst = line.split('\t')
+    if len(lst) >= 5:
+        tf0     = lst[1].upper().strip()
+        target0 = lst[4].upper().strip()
+        tf_lst = tf0.split('/')
+        target_lst = target0.split('/')
+        for tf in tf_lst:
+            for target in target_lst:
+                if tf.startswith('AT') and target.startswith('AT'):
+                    k = target + '.' + tf
+                    if k in d:
+                        #print('Warning at line %d  ' % (count))
+                        duplicate += 1
+                    else:
+                        d[k] = [target, tf, sample_id]
+    count += 1
+
+
+print('pairs %d' % len(d))
+print('duplicate %d' % (duplicate))
+for k in sorted(d.keys()):
+    print('\t'.join(d[k]))
+