Python SequenceList.read_listの例

コード例 #1

ファイル: test_integration.py プロジェクト: Duke-GCB/TF-DNA-PredictionsDB

    def test_sequence_list(self):
        FASTA_DATA1 = """>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA
CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG"""
        FASTA_DATA2 = """>stuff
AAACCCGGGG"""
        db = create_db_connection(TestWithPostgres.config.dbconfig)
        sequence_list1_uuid = SequenceList.create_with_content_and_title(db, FASTA_DATA1, "mystuff")
        sequence_list2_uuid = SequenceList.create_with_content_and_title(db, FASTA_DATA2, "mystuff2")
        seq_list1 = SequenceList.read_list(db, sequence_list1_uuid)
        seq_list2 = SequenceList.read_list(db, sequence_list2_uuid)
        self.assertEqual(FASTA_DATA1, seq_list1.content)
        self.assertEqual("mystuff", seq_list1.title)
        self.assertEqual("mystuff2", seq_list2.title)

コード例 #2

    def test_sequence_list(self):
        FASTA_DATA1 = """>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA
CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG"""
        FASTA_DATA2 = """>stuff
AAACCCGGGG"""
        db = create_db_connection(TestWithPostgres.config.dbconfig)
        sequence_list1_uuid = SequenceList.create_with_content_and_title(db, FASTA_DATA1, "mystuff")
        sequence_list2_uuid = SequenceList.create_with_content_and_title(db, FASTA_DATA2, "mystuff2")
        seq_list1 = SequenceList.read_list(db, sequence_list1_uuid)
        seq_list2 = SequenceList.read_list(db, sequence_list2_uuid)
        self.assertEqual(FASTA_DATA1, seq_list1.content)
        self.assertEqual("mystuff", seq_list1.title)
        self.assertEqual("mystuff2", seq_list2.title)