# 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)