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#!/usr/bin/env python
"""Unit tests for the bowtie default output parser.
Compatible with bowtie version 0.12.5
"""
from cogent.parse.bowtie import BowtieOutputParser, BowtieToTable
from cogent.util.unit_test import TestCase, main
from cogent import LoadTable
__author__ = "Gavin Huttley, Anuj Pahwa"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight","Peter Maxwell", "Gavin Huttley", "Anuj Pahwa"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Development"
fname = 'data/bowtie_output.map'
expected = [['GAPC_0015:6:1:1283:11957#0/1', '-', 'Mus', 66047927, 'TGTATATATAAACATATATGGAAACTGAATATATATACATTATGTATGTATATATGTATATGTTATATATACATA', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII', 0, ['55:A>G', '64:C>A']],
['GAPC_0015:6:1:1394:18813#0/1', '+', 'Mus', 77785518, 'ATGAAATTCCTAGCCAAATGGATGGACCTGGAGGGCATCATC', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII', 447, []],
['GAPC_0015:6:1:1560:18056#0/1', '+', 'Mus', 178806665, 'TAGATAAAGGCTCTGTTTTTCATCATTGAGAAATTGTTATTTTTCTGATGTTATA', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII', 0, ['9:T>G']],
['GAPC_0015:6:1:1565:19849#0/1', '+', 'Mus', 116516430, 'ACCATTTGCTTGGAAAATTGTTTTCCAGCCTTTCACTCTGAG', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII', 141, []],
['GAPC_0015:6:1:1591:17397#0/1', '-', 'Mus', 120440696, 'TCTAAATCTGTTCATTAATTAAGCCTGTTTCCATGTCCTTGGTCTTAAGACCAATCTGTTATGCGGGTGTGA', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII', 0, ['70:A>C', '71:G>T']]]
class BowtieOutputTest(TestCase):
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_psl_to_table(self):
"""make sure that the table is built without any errors"""
table = BowtieToTable(fname)
def test_getting_seq_coords(self):
"""get correct information from the table"""
table = BowtieToTable(fname)
index = 0
for row in table:
query_name = row['Query Name']
strand_direction = row['Strand Direction']
query_offset = row['Offset']
self.assertEqual(query_name, expected[index][0])
self.assertEqual(strand_direction, expected[index][1])
self.assertEqual(query_offset, expected[index][3])
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]))
if __name__ == "__main__":
main()
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