1 files changed, 58 insertions, 0 deletions
diff --git a/Code/process_3way_interaction2.py b/Code/process_3way_interaction2.py
new file mode 100644
index 0000000..7ce26b3
--- /dev/null
+++ b/Code/process_3way_interaction2.py
@@ -0,0 +1,58 @@
+# Purpose: convert results from three-way interaction analysis to edge format.
+# Usage: python process_3way_interaction.py ../Data/information/summary.txt > edges.txt.interaction.seeddata
+# Create on 9 Aug 2019 by Hui Lan <lanhui@zjnu.edu.cn>
+
+from geneid2name import make_gene_name_AGI_map_dict, get_gene_name
+
+def get_2tf_1target_1score(s):
+    '''
+    s looks like  '398:  ( AT3G10490;AT3G10480,  AT1G03970,  AT5G20910 )  10.41  2'
+    '''
+
+    lst = s.split()
+    tf1_all = lst[2]
+    tf2_all = lst[3]
+    target = lst[4]
+    score = lst[6]
+    result = []    
+    for tf1 in tf1_all.split(';'):
+        tf1 = tf1.replace(',', '')
+        for tf2 in tf2_all.split(';'):
+            tf2 = tf2.replace(',', '')
+            result.append((tf1, tf2, target, score))
+
+    return result
+
+## main
+import sys
+from datetime import datetime
+
+f = open(sys.argv[1])
+lines = f.readlines()
+f.close()
+
+
+agi2name_dict = make_gene_name_AGI_map_dict('../Data/information/AGI-to-gene-names_v2.txt')
+
+result = ''
+for line in lines[2:]:
+    line = line.strip()
+    lst = get_2tf_1target_1score(line)
+    for t in lst:
+        tf1, tf2, target, interaction_score_str = t
+        if tf1.startswith('AT') and tf2.startswith('AT') and target.startswith('AT'):
+            target_str = target + ' ' + get_gene_name(target, agi2name_dict)
+            tf1_str    = tf1   + ' ' + get_gene_name(tf1,     agi2name_dict)
+            tf2_str    = tf2   + ' ' + get_gene_name(tf2,     agi2name_dict)    
+            score_str  = '0.6'
+            cond_str   = '.'
+            curr_date  =  datetime.now().strftime('%Y%m%d')
+            method_or_tissue = 'interact.with.%s' % (tf2   + '(' + get_gene_name(tf2,     agi2name_dict) + ')')
+            s = '\t'.join([target_str, tf1_str, score_str, 'mix', '138', cond_str, '.', curr_date, interaction_score_str.replace('-',''), method_or_tissue])
+            result += s + '\n'
+            method_or_tissue = 'interact.with.%s' % (tf1   + '(' + get_gene_name(tf1,     agi2name_dict) + ')')
+            s = '\t'.join([target_str, tf2_str, score_str, 'mix', '138', cond_str, '.', curr_date, interaction_score_str.replace('-',''), method_or_tissue])
+            result += s + '\n'
+    
+
+print(result)