def run_meme():
print('\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~')
print('started running MEME ...')
config = get_config()
output_path = config['outputs']['path']
run_mode = config['settings']['mode']
meme_mode = config['settings']['meme_mode']
motif_min_width = config['settings']['motif_min_width']
motif_max_width = config['settings']['motif_max_width']
motif_evalue = config['settings']['motif_evalue']
number_of_motifs = config['settings']['number_of_motifs']
if motif_evalue == 'default':
evalue = ''
else:
evalue = '-evt %s' %motif_evalue
coexpression_file = output_path + 'coexpression_with_SFs_%s.txt'%run_mode
coexpression_df = pd.read_csv(coexpression_file, sep='\t')
SFs = list(set(coexpression_df.SF_id.values))
scripts_outlines = []
Rs = ['R1','R2','R3','R4']
for sf in SFs:
for R in Rs:
dir_name = 'meme_' + R + '_' + sf
input_seq_path = output_path + sf + '/' + R + '_' + sf + '.fasta'
output_meme_path = output_path + sf + '/' + dir_name
#if dir_name in os.listdir(output_path + sf):
# print('%s is already processed' %sf)
#else:
print('~~~~~~~~~~')
cmd = 'meme %s -o %s -dna -minw %s -maxw %s -maxsize 200000 -mod %s -nmotifs %s %s ' %(input_seq_path,output_meme_path,motif_min_width,motif_max_width,meme_mode,number_of_motifs,evalue)
scripts_outlines.append(cmd + '\n')
print cmd
os.system(cmd)
print('processing %s is done ' %sf)
print('---------------------------------\n')
scripts_file = open(output_path + 'meme_script.sh','w')
scripts_file.writelines(scripts_outlines)
scripts_file.close()
#run_meme()
__author__ = 'Delasa'
import pandas as pd
import os
import os.path as path
import numpy as np
from load_data import get_config
config = get_config()
data_path = config['data']['path']
output_path = config['outputs']['path']
run_mode = config['settings']['mode']
def find_cosplied_transcipts():
coexpression_file = output_path + 'coexpression_with_SFs_%s.txt' % run_mode
coexpression_df = pd.read_csv(coexpression_file, sep='\t')
SFs = list(set(coexpression_df.SF_id.values))
print '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
print('started making cosplicing netwoks ...')
results_dfs = []
for sf in SFs:
meme_output_path = output_path + sf + '/'
meme_results = os.listdir(meme_output_path)
for meme_res in meme_results:
if path.isdir(meme_output_path + meme_res):
#print 'processing ',meme_res, ' started'
status = None
if meme_res.lstrip('meme_').find('R1') == 0:
status = 'R1'
elif meme_res.lstrip('meme_').find('R2') == 0:
status = 'R2'