for input_f in inputFiles:
if zipfile.is_zipfile(input_f):
extract_zip_file(input_f, self.path_runs.get_path_execution())
else:
try:
inF = gzip.GzipFile(input_f, 'rb')
f = inF.read()
inF.close()
if f:
extract_gz_file(input_f, self.path_runs.get_path_execution())
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
else:
copy_pdbs_from_input(
self.path_runs.get_path_execution(),
self.opts.htmlfiledir,
self.opts.inputnames,
self.opts.inputPDBs)
if(self.opts.renameAtoms == 'true'):
if not rename_atoms(
self.path_runs.get_path_execution(),
self.opts.galaxyroot):
raise Exception("The script to rename the atoms finished wrong.")
if(self.opts.checkStructures == 'true'):
if not check_pdb(
self.path_runs.get_path_execution(),
self.opts.galaxyroot):
raise Exception("The script to check the structure finished wrong.")