brain: add python and R code to local repository.

1 files changed, 48 insertions, 0 deletions

diff --git a/Code/process_3way_interaction.py b/Code/process_3way_interaction.py
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+# Purpose: convert results from three-way interaction analysis to edge format.
+# Usage: python process_3way_interaction.py output20160911.txt > edges.txt.interaction.wiggelab.timecourse
+# 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 'AT1G73870_AT1G73870, AT5G10570_AT5G10570, AT2G05100_LHCB2.1	19.287 | 0.843 0.998 0.155 | -0.915 0.924 1.839 | 0.918 -0.419'
+    '''
+    lst = s.split()
+    tf1 = lst[0].split('_')[0]
+    tf2 = lst[1].split('_')[0]
+    target = lst[2].split('_')[0]
+    score = lst[3]
+    return (tf1, tf2, target, score)
+
+
+## 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:
+    line = line.strip()
+    tf1, tf2, target, interaction_score_str = get_2tf_1target_1score(line)
+    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  = '0.5'
+    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', '15', 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', '15', cond_str, '.', curr_date, interaction_score_str.replace('-',''), method_or_tissue])
+    result += s + '\n'
+    
+
+print(result)