# 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)