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# Usage: python slice_binding_to_JSON.py parameter_for_net.txt
import sys, os, operator, itertools
import numpy as np
import json
JSON_DIR = '../Data/history/bind/json2' # contains json for all genes
GLB_PARAM_SYMBOL = '%%'
DATA_SYMBOL = '@'
def read_matrix_data(fname):
'''
fname - a file, first line is head, first column is row name.
'''
lineno = 0
colid = []
rowid = []
d = {} # {gene1:{cond1:val1, cond2:val2, ...}, gene2: {...}, ...}
d2 = {} # {cond1:{gene1:val1, gene2:val2, ...}, cond2: {...}, ...}
d3 = {} # {gene1: [], gene2: [], ...}
d4 = {} # {cond1:[], cond2:[], ...}
f = open(fname)
lines = f.readlines()
f.close()
head_line = lines[0].strip()
lst = head_line.split()
colid = lst[1:]
for c in colid:
d2[c] = {}
d4[c] = []
for line in lines[1:]:
line = line.strip()
lst = line.split()
g = lst[0]
rowid.append(g)
d[g] = {}
levels = lst[1:]
if len(levels) != len(colid):
print('Incomplete columns at row %s' % (g))
sys.exit()
d3[g] = []
for i in range(len(colid)):
c = colid[i]
d[g][c] = float(levels[i])
d2[c][g] = float(levels[i])
d3[g].append(float(levels[i]))
d4[c].append(float(levels[i]))
lineno += 1
d_return = {}
d_return['xy'] = d # first gene, then condition
d_return['yx'] = d2 # first condition, then gene
d_return['xx'] = d3 # each item is an array of gene expression levels, i.e., each item is a row
d_return['yy'] = d4 # each item is an array of gene expression levels, i.e., each item is a column
d_return['nrow'] = lineno - 1
d_return['ncol'] = len(colid)
d_return['rowid'] = rowid
d_return['colid'] = colid
d4_sorted = {}
for k in d4:
d4_sorted[k] = sorted(d4[k], reverse=True)
d_return['yy_sorted'] = d4_sorted
return d_return
# read paramters
def get_key_value(s):
lst = s.split('=')
k, v = lst[0], lst[1]
return (k.strip(), v.strip())
def get_value(s, delimit):
lst = s.split(delimit)
return lst[1].strip()
def read_info_data(fname):
''' Read chip-seq data information '''
if not os.path.exists(fname):
print('%s not exists.' % (fname) )
sys.exit()
d = {'ID_LIST':[]}
f = open(fname)
lines = f.readlines()
f.close()
for line in lines:
line = line.strip()
if line == '' or line.startswith('#') or line.startswith('%'):
continue
if line.startswith(DATA_SYMBOL):
s = line[line.rfind(DATA_SYMBOL[-1])+1:]
s = s.strip()
if s in d:
print('ID %s duplicate' % (s))
sys.exit()
d[s] = {'PROTEIN_ID':'', 'PROTEN_NAME':'', 'DATA_NAME':'', 'DATA_FORMAT':'', 'DESCRIPTION':'', 'LOCATION':'', 'NOTE':''}
d['ID_LIST'].append(s)
if line.startswith('DESCRIPTION:'):
d[s]['DESCRIPTION'] = get_value(line, ':')
elif line.startswith('PROTEN_NAME:'):
d[s]['PROTEN_NAME'] = get_value(line, ':')
elif line.startswith('PROTEIN_ID:'):
d[s]['PROTEIN_ID'] = get_value(line, ':')
elif line.startswith('DATA_NAME:'):
d[s]['DATA_NAME'] = get_value(line, ':')
elif line.startswith('DATA_FORMAT:'):
d[s]['DATA_FORMAT'] = get_value(line, ':')
elif line.startswith('LOCATION:'):
d[s]['LOCATION'] = get_value(line, ':')
elif line.startswith('NOTE:'):
d[s]['NOTE'] = get_value(line, ':')
return d
def make_global_param_dict(fname):
f = open(fname)
d = {}
for line in f:
line = line.strip()
if line.startswith(GLB_PARAM_SYMBOL):
s = line[line.rfind(GLB_PARAM_SYMBOL[-1])+1:]
lst = s.split('\t') # separate items by TAB
for x in lst:
if x != '':
k, v = get_key_value(x)
d[k] = v
f.close()
return d
def make_json_file(bind_dict, bind_info_dict, dir_name, glb_param_dict):
if not os.path.isdir(dir_name): # create the directory if not exist
os.makedirs(dir_name)
d = bind_dict['xy']
col_name_lst = bind_dict['colid']
row_name_lst = bind_dict['rowid']
for g in row_name_lst:
#print(g)
d2 = d[g]
d3 = {}
for k in sorted(d2.keys()):
data_type = bind_info_dict[k]['DATA_FORMAT'].upper()
if data_type == 'NARROWPEAK':
data_type = 'NP' # short name for narrowPeak
value = d2[k]
d3[k] = {'v':value, 't':data_type}
filename = os.path.join(dir_name, g + '.json')
with open(filename, 'w') as f:
json.dump(d3, f)
### main
param_file = sys.argv[1] # a single prameter file
glb_param_dict = make_global_param_dict(param_file)
#print('Read binding matrix ...')
binding_dict = read_matrix_data(glb_param_dict['BINDING_MATRIX'])
bind_info_dict = read_info_data(glb_param_dict['BINDING_INFO'])
#print('Make json files ...')
make_json_file(binding_dict, bind_info_dict, JSON_DIR, glb_param_dict)
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