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# Utility functions
# Purpose: check what new edges have been created today.
# Created by Hui on 20 July 2021
import os
import shutil
import mmap
from datetime import datetime
def get_edge_set(fname):
result = set()
with open(fname) as f:
for line in f:
line = line.strip()
lst = line.split('\t')
if len(lst) == 10:
target_id = lst[0].split()[0].upper()
tf_id = lst[1].split()[0].upper()
result.add(target_id + '_' + tf_id)
return result
def make_new_edges_file(Sold, Snew, fname_new, output_file):
Sdiff = Snew.difference(Sold)
result = []
with open(fname_new) as f:
for line in f:
line = line.strip()
lst = line.split('\t')
if len(lst) == 10:
target_id = lst[0].split()[0].upper()
tf_id = lst[1].split()[0].upper()
if target_id + '_' + tf_id in Sdiff: # this is a new edge line, keep it
result.append(line)
with open(output_file, 'w') as f:
header = '\t'.join(['target_id target_name', 'source_id source_name', 'score', 'type of score', 'RNA-seqs', 'ChIP-seq', 'Log likelihood', 'Date', 'Strength', 'Inference method']) + '\n'
f.write(header)
for line in result:
f.write(line + '\n')
f.write('*** Number of newly added edges: %d. Last modification date: %s. ***\n' % (len(result), datetime.now().strftime('%Y-%m-%d %H:%M')))
def make_paths(s):
if not os.path.isdir(s):
os.makedirs(s)
def write_first_column(lst, fname):
with open(fname, 'w') as f:
for x in lst:
f.write(x + '\n')
def append_column_fast(basefile, col):
''' Append col to basefile. If basefile does not exist, then create it and col will be basefile's first column.'''
if not os.path.exists(basefile):
with open(basefile, 'w') as f:
count = 0
for x in col:
f.write(x + '\n')
count += 1
return count
with open(basefile) as f:
lines = f.readlines()
if len(lines) != len(col):
return
count = 0
with open(basefile, 'w') as f:
for line in lines:
line = line.strip()
new_line = line + '\t' + col[count] + '\n'
count += 1
f.write(new_line)
return count
def append_column_fast2(basefile, col):
''' Append col to basefile. If basefile does not exist, then create it and col will be basefile's first column.'''
if not os.path.exists(basefile):
with open(basefile, 'w') as f:
count = 0
for x in col:
f.write(x + '\n')
count += 1
return count
with open(basefile) as f:
with mmap.mmap(f.fileno(), length=0, access=mmap.ACCESS_READ) as mmap_f:
lines = mmap_f.read().split(b'\n')[:-1]
if len(lines) != len(col):
return
count = 0
content = ''
with open(basefile, 'w') as f:
for line in lines:
line = line.decode().strip()
new_line = line + '\t' + col[count] + '\n'
content += new_line
count += 1
f.write(content)
return count
if __name__ == '__main__':
S2 = get_edge_set('/home/lanhui/brain/Data/temp/edges.txt')
S1 = get_edge_set('/home/lanhui/brain/Data/temp/edges.txt.old')
make_new_edges_file(S1, S2, '/home/lanhui/brain/Data/temp/edges.txt', 'mynewedges.txt')
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