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import os
from pyfaidx import Faidx, Fasta, FetchError
from nose.tools import raises
from unittest import TestCase
path = os.path.dirname(__file__)
os.chdir(path)
class TestFeatureBuffer(TestCase):
def setUp(self):
pass
def tearDown(self):
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_buffer_false(self):
fasta = Fasta('data/genes.fasta', strict_bounds=True)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
assert result == expect
def test_buffer_true(self):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'.lower()
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:150].seq.lower()
assert result == expect
def test_buffer_exceed(self):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
expect = 'atgacatcattttccacctctgctcagtgttcaacatctgacagtgcttgcaggatctctcctggacaaatcaatcaggtacgaccaaaactgccgcttttgaagattttgcatgcagcaggtgcgcaaggtgaaatgttcactgttaaagaggtcatgcactatttaggtcagtacataatggtgaagcaactttatgatcagcaggagcagcatatggtatattgtggtggagatcttttgggagaactactgggacgtcagagcttctccgtgaaagacccaagccctctctatgatatgctaagaaagaatcttgtcactttagccactgctactacagcaaagtgcagaggaaagttccacttccagaaaaagaactacagaagacgatatcccc'
result = fasta['gi|557361099|gb|KF435150.1|'][0:400].seq.lower()
assert result == expect
@raises(FetchError)
def test_bounds_error(self):
fasta = Fasta('data/genes.fasta', read_ahead=300, strict_bounds=True)
result = fasta['gi|557361099|gb|KF435150.1|'][100-1:15000].seq.lower()
@raises(ValueError)
def test_buffer_value(self):
Fasta('data/genes.fasta', read_ahead=0.5)
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