def test_seqence_contains_function_no_file(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
fasta_record.add_sequence_line("AAAT")
fasta_record.add_sequence_line("TAAA")
self.assertTrue(fasta_record.sequence.contains("ATTA"))
self.assertFalse(fasta_record.sequence.contains("ACCA"))
def test_string_representation(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
fasta_record.add_sequence_line("atta\n")
fasta_record.add_sequence_line("TAAT")
self.assertEqual(str(fasta_record),
'\n'.join([">seq101|testing", "atta", "TAAT"]))
def test_seqence_contains_function_with_regex_no_file(self):
import re
regex_match = re.compile(r"A[T]{2}A")
regex_no_match = re.compile(r"A[T]{3}A")
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
fasta_record.add_sequence_line("AAAT")
fasta_record.add_sequence_line("TAAA")
self.assertTrue(fasta_record.sequence.contains(regex_match))
self.assertFalse(fasta_record.sequence.contains(regex_no_match))
def test_len_when_empty(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertEqual(len(fasta_record), 0)
def test_len(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
fasta_record.add_sequence_line("atta\n")
fasta_record.add_sequence_line("TAAT")
self.assertEqual(len(fasta_record), 8)
def test_seqence_type(self):
from tinyfasta import FastaRecord, Sequence
fasta_record = FastaRecord(">seq101|testing\n")
self.assertTrue(isinstance(fasta_record.sequence, Sequence))
def test_description_type(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertTrue(
isinstance(fasta_record.description, FastaRecord.Description))
def test_description(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertEqual(str(fasta_record.description), ">seq101|testing")
def test_FastaRecord_initialisation(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertTrue(isinstance(fasta_record, FastaRecord))
