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# Copyright 2012 by Jeff Hussmann. All rights reserved.
# Revisions copyright 2013 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import re
import unittest
from Bio import SeqIO
# sffinfo E3MFGYR02_random_10_reads.sff | sed -n '/>\|Run Prefix\|Region\|XY/p'
test_data = """
>E3MFGYR02JWQ7T
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 3946_2103
>E3MFGYR02JA6IL
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 3700_3115
>E3MFGYR02JHD4H
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 3771_2095
>E3MFGYR02GFKUC
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2520_2738
>E3MFGYR02FTGED
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2268_2739
>E3MFGYR02FR9G7
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2255_0361
>E3MFGYR02GAZMS
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2468_1618
>E3MFGYR02HHZ8O
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2958_1574
>E3MFGYR02GPGB1
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2633_0607
>E3MFGYR02F7Z7G
Run Prefix: R_2008_01_09_16_16_00_
Region #: 2
XY Location: 2434_1658"""
class TestUAN(unittest.TestCase):
def setUp(self):
self.records = [record for record in SeqIO.parse('Roche/E3MFGYR02_random_10_reads.sff', 'sff')]
self.test_annotations = {}
for line in test_data.splitlines():
fields = re.split(r"\s+", line.strip())
if '>' in line:
current_name = fields[0].lstrip('>')
self.test_annotations[current_name] = {}
elif 'Prefix' in line:
time_list = [int(v) for v in fields[2].split('_')[1:-1]]
self.test_annotations[current_name]["time"] = time_list
elif 'Region' in line:
region = int(fields[-1])
self.test_annotations[current_name]["region"] = region
elif 'XY' in line:
x, y = [int(v) for v in fields[-1].split('_')]
self.test_annotations[current_name]["coords"] = (x, y)
def test_time(self):
for record in self.records:
self.assertEqual(record.annotations["time"], self.test_annotations[record.name]["time"])
def test_region(self):
for record in self.records:
self.assertEqual(record.annotations["region"], self.test_annotations[record.name]["region"])
def test_coords(self):
for record in self.records:
self.assertEqual(record.annotations["coords"], self.test_annotations[record.name]["coords"])
class TestConcatenated(unittest.TestCase):
def test_parses_gzipped_stream(self):
import gzip
count = 0
fh = gzip.open("Roche/E3MFGYR02_random_10_reads.sff.gz", 'rb')
for record in SeqIO.parse(fh, 'sff'):
count += 1
self.assertEqual(10, count)
def test_parse1(self):
count = 0
caught = False
try:
for record in SeqIO.parse("Roche/invalid_greek_E3MFGYR02.sff", "sff"):
count += 1
except ValueError as err:
self.assertTrue("Additional data at end of SFF file, perhaps "
"multiple SFF files concatenated? "
"See offset 65296" in str(err), err)
caught = True
self.assertTrue(caught, "Didn't spot concatenation")
self.assertEqual(count, 24)
def test_index1(self):
try:
d = SeqIO.index("Roche/invalid_greek_E3MFGYR02.sff", "sff")
except ValueError as err:
self.assertTrue("Additional data at end of SFF file, perhaps "
"multiple SFF files concatenated? "
"See offset 65296" in str(err), err)
else:
raise ValueError("Indxing Roche/invalid_greek_E3MFGYR02.sff should fail")
def test_parse2(self):
count = 0
caught = False
try:
for record in SeqIO.parse("Roche/invalid_paired_E3MFGYR02.sff", "sff"):
count += 1
except ValueError as err:
self.assertTrue("Your SFF file is invalid, post index 5 byte "
"null padding region ended '.sff' which could "
"be the start of a concatenated SFF file? "
"See offset 54371" in str(err), err)
caught = True
self.assertTrue(caught, "Didn't spot concatenation")
self.assertEqual(count, 20)
def test_index2(self):
try:
d = SeqIO.index("Roche/invalid_paired_E3MFGYR02.sff", "sff")
except ValueError as err:
self.assertTrue("Your SFF file is invalid, post index 5 byte "
"null padding region ended '.sff' which could "
"be the start of a concatenated SFF file? "
"See offset 54371" in str(err), err)
else:
raise ValueError("Indxing Roche/invalid_paired_E3MFGYR02.sff should fail")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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