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) )
