Python SequenceListItems.find_sequence_items Beispiele

Beispiel #1

Datei: test_sequencelist.py Projekt: Duke-GCB/iMADS

 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'])

Beispiel #2

Datei: test_sequencelist.py Projekt: Duke-GCB/iMADS

    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])