def test_extract_mutations_from_lines_to_file_w_non_default_extractor(self):
"""extract_mutations_from_lines_to_file: functions w baseline extractor
"""
from tempfile import mktemp
from os import remove
actual_output_filepath = mktemp()
# BaselineMutationExtractor does not provide spans -- requesting
# them results in a properly handled error
self.assertRaises(MutationFinderError,\
extract_mutations_from_lines_to_file,self.fake_input_file,\
actual_output_filepath,BaselineMutationExtractor(),\
store_spans=True)
# remove the temp file that was created
remove(actual_output_filepath)
actual_output_filepath = mktemp()
extract_mutations_from_lines_to_file(self.fake_input_file,\
actual_output_filepath,BaselineMutationExtractor())
actual_output = list(open(actual_output_filepath))
# remove the temp file that was created
remove(actual_output_filepath)
# compare the lines in the fake output file with those in the
# real output file
expected_output = ['id1','id2\tG88Y\tG88Y\tW42A\tW42A',\
'id3','id4','id5']
for actual,expected in zip(actual_output,expected_output):
self.assertEqual(actual.strip(),expected)
def test_extract_mutations_from_lines_to_file_w_spans(self):
"""extract_mutations_from_lines_to_file: spans"""
from tempfile import mktemp
from os import remove
actual_output_filepath = mktemp()
extract_mutations_from_lines_to_file(self.fake_input_file,\
actual_output_filepath,self.mf,store_spans=True)
actual_output = list(open(actual_output_filepath))
# remove the temp file that was created
remove(actual_output_filepath)
# compare the lines in the fake output file with those in the
# real output file
for i,line in zip(range(len(actual_output)),actual_output):
self.assertEqual(line.strip(),self.fake_output_file_w_spans[i])
