def load(cls, treefile, schema=None):
if not os.path.isfile(treefile):
print 'No tree file found.'
return None
try: return dp.Tree.get(path=treefile, schema=cls.schema(treefile, schema))
except Exception, e:
print 'Error while loading %s:\n%s' % (treefile, estr(e))
return None
def blast(cls, command, **kwargs):
'''Generic wrapper for blast commandline programs'''
results_file = kwargs.pop('save_results_to', None)
parse_results = kwargs.pop('parse_results', False)
if results_file: bout = results_file
else:
parse_results = True
bout = mktmp_name('.xml')
try:
cline = cls._clines[command]
cmd = cline(outfmt=5, out=bout, **kwargs)
out, err = cmd()
if err:
print ('\nError message from %s:\n%s\n%s\n%s'
% (command, cmd, out, err))
if parse_results:
with open(bout) as inp:
results = list(NCBIXML.parse(inp))
return results
except Exception, e:
print '\nError while performing local %s:\n%s' % (command, estr(e))
return None
def aborted(abort_event):
try: return abort_event.is_set()
except IOError, e:
print 'IOError while accessing abort Event:\n%s' % estr(e)#test
return True