1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
|
# 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)
|
