def test_find_items_simple(self):
data = "ACGT\nAAACCCGGTT\nTTTTTTTT"
items = SequenceListItems.find_sequence_items(SequenceListItems.make_fasta(data))
self.assertEqual(3, len(items))
self.assertEqual(1, items[0]['idx'])
self.assertEqual('seq1', items[0]['name'])
self.assertEqual('ACGT', items[0]['sequence'])
self.assertEqual(2, items[1]['idx'])
self.assertEqual('seq2', items[1]['name'])
self.assertEqual('AAACCCGGTT', items[1]['sequence'])
self.assertEqual(3, items[2]['idx'])
self.assertEqual('seq3', items[2]['name'])
self.assertEqual('TTTTTTTT', items[2]['sequence'])
def test_find_items_fasta(self):
data = """>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA
CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG
GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGACCCCTG
GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCGGAGGA"""
items = SequenceListItems.find_sequence_items(SequenceListItems.make_fasta(data))
self.assertEqual(2, len(items))
self.assertEqual(1, items[0]['idx'])
self.assertEqual('HSBGPG', items[0]['name'])
self.assertEqual('GGCAGATTCC', items[0]['sequence'][:10])
self.assertEqual(2, items[1]['idx'])
self.assertEqual('HSGLTH1', items[1]['name'])
self.assertEqual('CCACTGCACT', items[1]['sequence'][:10])
def test_make_fasta(self):
values = [
#input output
("ACGT\n", ">seq1\nACGT"),
("ACGT", ">seq1\nACGT"),
("ACGT\nAACC\n", ">seq1\nACGT\n>seq2\nAACC"),
(">stuff\nACGT\n", ">stuff\nACGT"),
]
for in_value, out_value in values:
result = SequenceListItems.make_fasta(in_value)
self.assertEqual(out_value, result)