sys.exit(1) filename_cmd_tmpl = os.path.join(MSTB_HOME,'tmpl','inspect.cmd') f_cmd_tmpl = open(filename_cmd_tmpl,'r') cmd_tmpl = ''.join( f_cmd_tmpl.readlines() ) f_cmd_tmpl.close() filename_in_tmpl = os.path.join(MSTB_HOME,'tmpl','inspect.in') f_in_tmpl = open(filename_in_tmpl,'r') in_tmpl = ''.join( f_in_tmpl.readlines() ) f_in_tmpl.close() # Blake additions 3/11/2012 import numpy as np n_per_run = 25 mzxmls_all = helper.get_mzxml_list() nruns = np.floor(len(mzxmls_all) / n_per_run) + 1 for i in range(nruns): mzxmls = mzxmls_all[n_per_run*i:n_per_run*(i+1)] filename_run = os.path.join(CWD,'scripts','run-inspect-%s.sh' % i) f_run = open(filename_run,'w') f_run.write('#!/bin/bash\n') for basename_mzXML in mzxmls: filename_base = basename_mzXML.replace('.mzXML','') filename_in = os.path.join(CWD,dirname,'%s.inspect_in'%filename_base) filename_out = os.path.join(CWD,dirname,'%s.inspect_out'%filename_base) in_param = dict() in_param['DB_TRIE'] = conf['DB_TRIE'] in_param['FILENAME_MZXML'] = os.path.join(CWD,'mzXML',basename_mzXML)
sys.exit(1) filename_cmd_tmpl = os.path.join(MSTB_HOME,'tmpl','inspect.cmd') f_cmd_tmpl = open(filename_cmd_tmpl,'r') cmd_tmpl = ''.join( f_cmd_tmpl.readlines() ) f_cmd_tmpl.close() filename_in_tmpl = os.path.join(MSTB_HOME,'tmpl','inspect.in') f_in_tmpl = open(filename_in_tmpl,'r') in_tmpl = ''.join( f_in_tmpl.readlines() ) f_in_tmpl.close() filename_run = os.path.join(CWD,'scripts','run-inspect.sh') f_run = open(filename_run,'w') f_run.write('#!/bin/bash\n') for basename_mzXML in helper.get_mzxml_list(): filename_base = basename_mzXML.replace('.mzXML','') filename_in = os.path.join(CWD,dirname,'%s.inspect_in'%filename_base) filename_out = os.path.join(CWD,dirname,'%s.inspect_out'%filename_base) in_param = dict() in_param['DB_TRIE'] = conf['DB_TRIE'] in_param['FILENAME_MZXML'] = os.path.join(CWD,'mzXML',basename_mzXML) cmd_param = dict() cmd_param['PATH_INSPECT'] = conf['PATH_INSPECT'] cmd_param['DIR_INSPECT'] = conf['DIR_INSPECT'] cmd_param['FILENAME_IN'] = filename_in cmd_param['FILENAME_OUT'] = filename_out f_run.write( cmd_tmpl.format(**cmd_param) )