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# Usage: python validate_parameter_for_buildCmatrix.py
# Purpose: make sure all files exist.
# Hui 24 Jan 2018 Jinhua
import os, sys
import numpy as np
import glob
import time
import subprocess
from datetime import datetime
def get_value(s, delimit):
lst = s.split(delimit, 1) # only split at the first delimit
return lst[1].strip()
def get_key_value(s):
lst = s.split('=')
k, v = lst[0], lst[1]
return (k.strip(), v.strip())
def validate_gene_file(fname):
f = open(fname)
lines = f.readlines()
f.close()
for line in lines: # check all lines
line = line.strip()
lst = line.split('\t')
if len(lst) < 6:
print('Not enought fields: %s. Only %d are given. Each line must have gene_id, gene_name, chr, start, end, strand, description (optional). See prepare_gene_file.py in the documentation on how to prepare this file.' % (line, len(lst)))
sys.exit()
def validate_parameter_for_buildcmatrix(fname):
# first the file must exist
if not os.path.exists(fname):
print('CANNOT FIND %s.' % (fname))
sys.exit()
f = open(fname)
lines = f.readlines()
f.close()
d = {}
location_count = 0
for line in lines:
line = line.strip()
if line.startswith('%%'):
k, v = get_key_value(line[2:])
d[k] = v
if k == 'GENE_FILE' or k == 'CHR_INFO':
if not os.path.exists(v):
print('%s not exists.' % (v))
sys.exit()
if k == 'GENE_FILE':
validate_gene_file(v)
if k == 'DESTINATION':
if not os.path.isdir(v):
print('%s not exists.' % (v))
sys.exit()
if k == 'TARGET_RANGE':
if int(v) <= 0:
print('Target range (%d) must be greater than 0.' % (v))
sys.exit()
if line.startswith('LOCATION:'):
v = get_value(line, ':')
location_count += 1
if not os.path.exists(v):
print('Location %s does not exists.' % (v))
#sys.exit()
if not 'GENE_FILE' in d:
print('Must specify GENE_FILE.')
sys.exit()
if not 'DESTINATION' in d:
print('Must specify DESTINATION.')
sys.exit()
if not 'CHR_INFO' in d:
print('Must specify CHR_INFO.')
sys.exit()
if location_count == 0:
print('Must contain at least one ChIP-seq.')
sys.exit()
## main
PARAMETER_FOR_BUILDCMATRIX = '../Data/parameter/parameter_for_buildCmatrix.txt'
validate_parameter_for_buildcmatrix(PARAMETER_FOR_BUILDCMATRIX)
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