def exercise():
if (iotbx_mtz is None):
print \
"Skipping iotbx/examples/tst_mtz_free_flipper.py: ccp4io not available"
return
input_file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/l.mtz",
test=os.path.isfile)
if (input_file_name is None):
print "Skipping exercise(): input file not available"
return
label = "R-free-flags(-)"
mtz_free_flipper.run(args=[input_file_name], label=label)
mtz_free_flipper.run(args=["free_flipped_l.mtz"], label=label)
mtz_convert_free_to_work.run(args=[input_file_name], label=label)
spreadsheets = []
for file_name, expected in [
(input_file_name, (13469,1065,2323)),
("free_flipped_l.mtz", (1065,13469,2323)),
("free_flipped_free_flipped_l.mtz", (13469,1065,2323)),
("less_free_l.mtz", (14002,532,2323))]:
s = StringIO()
mtz_obj = iotbx_mtz.object(file_name=file_name)
mtz_obj.show_column_data(out=s, format="spreadsheet")
s = s.getvalue()
spreadsheets.append(s)
n_0, n_1, n_rest = 0, 0, 0
for line in s.splitlines()[1:]:
if (line.endswith(",0")): n_0 += 1
elif (line.endswith(",1")): n_1 += 1
else:
assert line.endswith(",")
n_rest += 1
assert mtz_obj.n_reflections() == n_0 + n_1 + n_rest
assert (n_0, n_1, n_rest) == expected
assert not show_diff(spreadsheets[0], spreadsheets[2])
assert spreadsheets[0] != spreadsheets[1]
msg.warning('problem while dumping joboption file to [%s]:\n%s',
dump_jobo, err)
from collections import namedtuple
Options = namedtuple('Options',
'oname use_recex_links do_clean_up athena_opts')
opts = Options(oname=output,
use_recex_links=use_recex_links,
do_clean_up=do_clean_up,
athena_opts=athena_opts)
sc, out = 1, "<N/A>"
msg.info('running dumper...')
sc,out = _run_jobo(jobo, msg, opts)
msg.info('dumper done')
if output != os.devnull:
msg.info('writing logfile: %s.log', output)
try:
with open('%s.log'%output, 'w') as f:
for l in out.splitlines():
print >> f, l
print >> f, "### EOF ###"
except Exception, err:
msg.warning('problem writing out logfile [%s.log]:\n%s',
output, err)
msg.info('bye.')
msg.info(':'*40)
return sc, out
