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# 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)
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