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_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_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_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_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_create_fasta_record(self):
from tinyfasta import FastaRecord
description = ">seq101|testing"
sequence = "ATCG"*30
fasta_record = FastaRecord.create(description, sequence)
self.assertEqual(str(fasta_record),
""">seq101|testing
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG""")
def test_create_fasta_record(self):
from tinyfasta import FastaRecord
description = ">seq101|testing"
sequence = "ATCG" * 30
fasta_record = FastaRecord.create(description, sequence)
self.assertEqual(
str(fasta_record), """>seq101|testing
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG""")
def test_update_description(self):
from tinyfasta import FastaRecord
description = FastaRecord.Description(">seq101|testing\n")
self.assertEqual(str(description), ">seq101|testing")
description.update(">seq102|testing\n")
self.assertEqual(str(description), ">seq102|testing")
description.update(">seq103|testing")
self.assertEqual(str(description), ">seq103|testing")
description.update(">seq104|testing")
self.assertEqual(str(description), ">seq104|testing")
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_Description_initialisation(self):
from tinyfasta import FastaRecord
description = FastaRecord.Description(">seq101|testing\n")
self.assertTrue(isinstance(description, FastaRecord.Description))
def test_FastaRecord_initialisation(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertTrue(isinstance(fasta_record, FastaRecord))
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_description(self):
from tinyfasta import FastaRecord
fasta_record = FastaRecord(">seq101|testing\n")
self.assertEqual(str(fasta_record.description), ">seq101|testing")
def test_str(self):
from tinyfasta import FastaRecord
description = FastaRecord.Description(">seq101|testing\n")
self.assertEqual(str(description), ">seq101|testing")
def test_content(self):
from tinyfasta import FastaRecord
description = FastaRecord.Description(">seq101|testing\n")
self.assertEqual(description._content, ">seq101|testing")
def test_Description_initialisation_withount_leading_arrow(self):
from tinyfasta import FastaRecord
description = FastaRecord.Description("seq101|testing\n")
self.assertEqual(str(description), ">seq101|testing")
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))
