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# Usage: python buildCmatrix.py parameter_for_buildCmatrix.txt > binding.txt
#
# Purpose: combine all binding columns into a matrix, binding.txt.
# Each ChIP-seq experiment has the following binding column file in
# the following format
#
# gene_id C0003000001450
# AT1G01010 0
# AT1G01020 0
# AT1G01030 0
# AT1G01040 0
# AT1G01046 0
# AT1G01050 0
# AT1G01060 0
# ...
#
# These column files are stored under DESTINATION in parameter_for_buildCmatrix.txt
# Created on 3 JAN 2017 hui SLCU
# Last modified 5 APR 2017 SLCU hui
# Last modified 6 Aug 2019 Hui Lan <lanhui@zjnu.edu.cn> [now accept a second command-line argument 'include-all']
import sys, os
from datetime import datetime
####################################
GLB_PARAM_SYMBOL = '%%'
LCL_PARAM_SYMBOL = '%'
DATA_SYMBOL = '@' # followed by data name, or condition name, should be unique
CHIP_SYMBOL = 'ChIP' # followed by ChIP peak file path
CHIP_GENE_SYMBOL = 'ChIP_GENE' # followed by ChIP protein name (in upper case, gene id or gene name)
RNA_SYMBOL = 'RNA' # followed by RNA data, a TPM table, first column is gene id, second column is TPM value
BIGWIG_SYMBOL = 'BIGWIG' # future work
DESCRI_SYMBOL = 'DESCRIPTION' # followed by data description
####################################
def get_key_value(s):
lst = s.split('=', 1)
k, v = lst[0], lst[1]
return (k.strip(), v.strip())
def get_value(s, delimit):
lst = s.split(delimit, 1)
return lst[1].strip()
def make_global_param_dict(fname):
f = open(fname)
d = {'GENE_FILE':'', 'TARGET_RANGE':'3000', 'FC':'2.0', 'PVALUE':'0.0001', 'QVALUE':'0.01', 'DESTINATION':'', 'REBUILD_LIST':[] } # change
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
if k == 'REBUILD_LIST' and v.lower() != 'all' and v != '':
d[k] = v.split() # make a list and rewrite d[k]
elif k == 'REBUILD_LIST':
d[k] = []
f.close()
return d
def make_data_dict(fname):
''' Scan parameter_for_buildCmatrix.txt and get its information into a dictionary, where key is ChIP-seq experiment ID, and value is a dictionary containing information for that experiment'''
# d = {'ID_LIST':[]} # keep a list of chip id's, such as C0001100007100
# f = open(fname)
# lines = f.readlines()
# f.close()
# for line in lines:
# line = line.strip()
# if line == '' or line.startswith('#'):
# continue
# if line.startswith(DATA_SYMBOL):
# s = line[line.rfind(DATA_SYMBOL[-1])+1:]
# s = s.strip() # s is ChIP-seq ID
# 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, ':')
# elif line.startswith(LCL_PARAM_SYMBOL) and not line.startswith(GLB_PARAM_SYMBOL):
# make_local_parameter(d[s]['PARAM'], line)
# return d
# Essentially the same as make_data_dict from get_binding.py
d = {'ID_LIST':[]} # keep a list of chip id's, such as C0001100007100
f = open(fname)
lines = f.readlines()
f.close()
for line in lines:
line = line.strip()
if line == '' or line.startswith('#'):
continue
if line.startswith(DATA_SYMBOL):
s = line[line.rfind(DATA_SYMBOL[-1])+1:]
s = s.strip()
if s in d: # ID is duplicate. Check paramter_for_buildCmatrix.txt
sys.exit()
d[s] = {'PROTEIN_ID':'', 'PROTEN_NAME':'', 'DATA_NAME':'', 'DATA_FORMAT':'', 'DESCRIPTION':'', 'LOCATION':'', 'NOTE':''}
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, ':')
if os.path.exists(d[s]['LOCATION']): # include this ID only when its file exists. It could happen the location no longer has that file.
d['ID_LIST'].append(s)
elif line.startswith('NOTE:'):
d[s]['NOTE'] = get_value(line, ':')
elif line.startswith(LCL_PARAM_SYMBOL) and not line.startswith(GLB_PARAM_SYMBOL):
make_local_parameter(d[s]['PARAM'], line)
d['ID_LIST'] = sorted(d['ID_LIST'])
return d
def make_chip_data(fname):
''' convert each binding column file into a dictionary '''
d = {}
if not os.path.exists(fname):
print('buildCmatrix: Cannot find file %s' % (fname))
sys.exit()
f = open(fname)
lines = f.readlines()
f.close()
for line in lines[1:]: # ignore first line, such as 'gene_id C0001100007100'
line = line.strip()
lst = line.split()
g = lst[0]
v = lst[1]
d[g] = v
return d
def get_update_date(s):
index = s.find('update:')
if index < 0:
return '00000000'
result = s[s.rfind('update:')+7:].strip()
if result.isdigit() and len(result) == 6:
return result
else:
return '00000000'
def make_table(gene_file, data_dict, glb_param_dict):
'''
Each line in gene file contains TAB-separated fields: gene_id, gene_name, chr, start, end, strand, description (optional)
'''
if glb_param_dict['REBUILD_LIST'] == []: # if not specified, use all
id_lst_all = data_dict['ID_LIST']
else:
id_lst_all = glb_param_dict['REBUILD_LIST']
# When we build binding.txt, we don' include ChIP data marked with 'obsolete' in its NOTE field.
id_lst = []
for i in id_lst_all:
note = data_dict[i]['NOTE'].lower()
curr_date = datetime.now().strftime('%Y%m%d')
include_this_id = not 'obsolete' in note \
and int(curr_date) - int(get_update_date(data_dict[i]['NOTE'])) < 7 # a ChIP-seq older than 7 days will be ignored.
if include_this_id or FORCE_INCLUDE_ALL: # don't include ChIP-seq marked with 'obsolete'
id_lst.append(i)
if id_lst == []:
print('buildCmatrix: ChIP-seq ID list is empty.')
sys.exit()
# head line of binding.txt
id_str = 'gene_id'
for myid in id_lst:
id_str += '\t' + myid
print(id_str)
chip_data_dict = {}
for myid in id_lst:
chip_file = os.path.join(glb_param_dict['DESTINATION'], myid + '.txt') # each binding column file has name such as C0001100007100.txt
chip_data = make_chip_data(chip_file)
chip_data_dict[myid] = chip_data
f = open(gene_file)
for line in f:
line = line.strip()
lst = line.split('\t')
gene_id = lst[0]
s0 = gene_id
for myid in id_lst:
if gene_id in chip_data_dict[myid]:
s0 += '\t' + chip_data_dict[myid][gene_id]
else:
s0 += '\t' + '-1'
print(s0)
f.close()
## main
param_file = sys.argv[1]
FORCE_INCLUDE_ALL = False
if len(sys.argv) > 2:
FORCE_INCLUDE_ALL = sys.argv[2].lower() == 'include-all'
global_param_dict = make_global_param_dict(param_file)
data_dict = make_data_dict(param_file)
make_table(global_param_dict['GENE_FILE'], data_dict, global_param_dict)
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