def _prepare_pictures(sub):
pictureslist = []
picfile = None
for key in sub.letter_annotations.keys():
np = dict()
np['picname'] = key
np['secondary_structure'] = sub.letter_annotations[key]
try:
picfile = run_rnaplot(seq=str(sub.seq),
structure=sub.letter_annotations[key],
format='svg')
with open(picfile) as f:
np['pic'] = "data:image/svg+xml;utf8," + f.read()
pictureslist.append(np)
remove_one_file_with_try(picfile)
except RNAplotException:
print("can't draw structure with RNAfold for {}.".format(sub.id))
except FileNotFoundError:
if picfile is not None:
print('cannot remove file: {}, file not found'.format(picfile))
except OSError:
if picfile is not None:
print('cannot remove file: {}, file is directory'.format(
picfile))
return pictureslist
def test_plot_gml(self):
run_rnaplot(self.seq, self.str, outfile=self.file, format="gml")
self.assertTrue(loadfile_len(self.file))
def test_basic(self):
run_rnaplot(self.seq, self.str, outfile=self.file)
self.assertTrue(loadfile_len(self.file))