def test_parsing(self):
"""make sure that the bowtie output file is parsed properly"""
parser = BowtieOutputParser(fname)
header = parser.next()
index = 0
for row in parser:
self.assertEqual(row, expected[index])
index += 1
def test_parsing(self):
"""make sure that the bowtie output file is parsed properly"""
parser = BowtieOutputParser(fname)
header = parser.next()
index = 0
for row in parser:
self.assertEqual(row, expected[index])
index += 1
def test_no_row_converter(self):
"""setting row_converter=None returns strings"""
# straight parser
parser = BowtieOutputParser(fname, row_converter=None)
header = parser.next()
for index, row in enumerate(parser):
query_offset = row[3]
other_matches = row[6]
self.assertEqual(query_offset, str(expected[index][3]))
self.assertEqual(other_matches, str(expected[index][6]))
# table
table = BowtieToTable(fname, row_converter=None)
for index, row in enumerate(table):
query_offset = row['Offset']
other_matches = row['Other Matches']
self.assertEqual(query_offset, str(expected[index][3]))
self.assertEqual(other_matches, str(expected[index][6]))
def test_no_row_converter(self):
"""setting row_converter=None returns strings"""
# straight parser
parser = BowtieOutputParser(fname, row_converter=None)
header = parser.next()
for index, row in enumerate(parser):
query_offset = row[3]
other_matches = row[6]
self.assertEqual(query_offset, str(expected[index][3]))
self.assertEqual(other_matches, str(expected[index][6]))
# table
table = BowtieToTable(fname, row_converter=None)
for index, row in enumerate(table):
query_offset = row['Offset']
other_matches = row['Other Matches']
self.assertEqual(query_offset, str(expected[index][3]))
self.assertEqual(other_matches, str(expected[index][6]))
