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"""
Tests for `bx.seq.fasta`.
"""
import unittest
from bx.seq import fasta
test_fa = "test_data/seq_tests/test.fa"
# Same sequence data as stored in test.fa
valid_seq = (
"TGGAGGCATTTGTGATTCAATAGATGCAGAAAGAAACCTTCCTAGAGCTG"
"GCGTTCTCTAACTAAAAGTGGAAAGTTCTGAGGAATGAGGACTGTTATAA"
"ATCCCACCCCACACCGCACCTTCTCCAGGGAAGTTTCATGGCCGTGAAGA"
"GGACAGAAAGTGAGAACCAAGATggaactgaataaacaagcttcacactg"
"ttagtttccccatatgcttaccttcccacagatgccaaccttggaggcct"
"aagaggcctagaatattatcctttgtctgatcatttctctacaaatttat"
"tgttctttgttaagatgctacataagcccaaattctaaccacccctttga"
"gttacccatcatcaagtttctcccatgtg"
)
valid_seq_len = len(valid_seq)
class FASTATestCase(unittest.TestCase):
def test_get(self):
fastafile = fasta.FastaFile(open(test_fa, "rb"))
check_get(fastafile, 0, valid_seq_len)
check_get(fastafile, 0, 40)
check_get(fastafile, valid_seq_len - 40, 40)
def check_get(fastafile, start, len):
assert fastafile.get(start, len) == valid_seq[start : start + len]
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