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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.parse.fastq import MinimalFastqParser
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
data = {
"GAPC_0015:6:1:1259:10413#0/1":
dict(seq='AACACCAAACTTCTCCACCACGTGAGCTACAAAAG',
qual=r'````Y^T]`]c^cabcacc`^Lb^ccYT\T\Y\WF'),
"GAPC_0015:6:1:1283:11957#0/1":
dict(seq='TATGTATATATAACATATACATATATACATACATA',
qual=r']KZ[PY]_[YY^```ac^\\`bT``c`\aT``bbb'),
"GAPC_0015:6:1:1284:10484#0/1":
dict(seq='TCAGTTTTCCTCGCCATATTTCACGTCCTAAAGCG',
qual=r'UM_]]U_]Z_Y^\^^``Y]`^SZ]\Ybb`^_LbL_'),
"GAPC_0015:6:1:1287:17135#0/1":
dict(seq='TGTGCCTATGGAAGCAGTTCTAGGATCCCCTAGAA',
qual=r'^aacccL\ccc\c\cTKTS]KZ\]]I\[Wa^T`^K'),
"GAPC_0015:6:1:1293:3171#0/1":
dict(seq="AAAGAAAGGAAGAAAAGAAAAAGAAACCCGAGTTA",
qual=r"b`bbbU_[YYcadcda_LbaaabWbaacYcc`a^c"),
"GAPC_0015:6:1:1297:10729#0/1":
dict(seq="TAATGCCAAAGAAATATTTCCAAACTACATGCTTA",
qual=r"T\ccLbb``bacc]_cacccccLccc\ccTccYL^"),
"GAPC_0015:6:1:1299:5940#0/1":
dict(seq="AATCAAGAAATGAAGATTTATGTATGTGAAGAATA",
qual=r"dcddbcfffdfffd`dd`^`c`Oc`Ybb`^eecde"),
"GAPC_0015:6:1:1308:6996#0/1":
dict(seq="TGGGACACATGTCCATGCTGTGGTTTTAACCGGCA",
qual=r"a]`aLY`Y^^ccYa`^^TccK_X]\c\c`caTTTc"),
"GAPC_0015:6:1:1314:13295#0/1":
dict(seq="AATATTGCTTTGTCTGAACGATAGTGCTCTTTGAT",
qual=r"cLcc\\dddddaaYd`T```bLYT\`a```bZccc"),
"GAPC_0015:6:1:1317:3403#0/1":
dict(seq="TTGTTTCCACTTGGTTGATTTCACCCCTGAGTTTG",
qual=r"\\\ZTYTSaLbb``\_UZ_bbcc`cc^[ac\a\T\ ".strip())# had to add space
}
class ParseFastq(TestCase):
def test_parse(self):
"""sequence and info objects should correctly match"""
for label, seq, qual in MinimalFastqParser('data/fastq.txt'):
self.assertTrue(label in data)
self.assertEqual(seq, data[label]["seq"])
self.assertEqual(qual, data[label]["qual"])
if __name__ == "__main__":
main()
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