Python _make_mini_otu_files Examples

Example #1

    def test_make_mini_otu_files(self):
        os.system("mkdir tmp")
        extension_seqs = list(skbio.io.read(self.extension_seqs,
                                            format='fasta'))

        _make_mini_otu_files(self.key_node,
                             self.extension_genus_dic_few,
                             extension_seqs)

        result = str(list(skbio.io.read('tmp/mini_seq_gt.fasta',
                                        format='fasta'))[0])

        os.system("rm -r tmp")
        self.assertEqual(result, 'TTAAAAAA')

Example #2

    def test_make_mini_otu_files(self):
        os.system("mkdir tmp")
        extension_seqs = list(
            skbio.io.read(self.extension_seqs, format='fasta'))

        with tempfile.TemporaryDirectory() as tmp:
            _make_mini_otu_files(self.key_node, self.extension_genus_dic_few,
                                 extension_seqs, tmp)

            result = str(
                list(skbio.io.read(tmp + "/mini_seq_gt.fasta",
                                   format='fasta'))[0])

        os.system("rm -r tmp")
        self.assertEqual(result, 'TTAAAAAA')

Example #3

File: test_hybridtree.py Project: JTFouquier/ghost-tree

    def test_make_mini_otu_files(self):
        os.system("mkdir tmp")
        extension_seqs = list(skbio.io.read(self.extension_seqs,
                                            format='fasta'))

        with tempfile.TemporaryDirectory() as tmp:
            _make_mini_otu_files(self.key_node,
                                 self.extension_genus_dic_few,
                                 extension_seqs, tmp)

            result = str(list(skbio.io.read(tmp + "/mini_seq_gt.fasta",
                                            format='fasta'))[0])

        os.system("rm -r tmp")
        self.assertEqual(result, 'TTAAAAAA')

Example #4

File: test_hybridtree.py Project: wasade/ghost-tree

 def test_make_mini_otu_files(self):
     os.system("mkdir tmp")
     self.extension_seqs = SequenceCollection.read(self.extension_seqs)
     result = _make_mini_otu_files(self.key_node,
                                   self.extension_genus_dic_few,
                                   self.extension_seqs)
     os.system("rm -r tmp")
     self.assertEqual(result, """>P1\nTTAAAAAA\n""")

Example #5

File: test_hybridtree.py Project: johnchase/hybrid_tree

 def test_make_mini_otu_files(self):
     os.system("mkdir tmp")
     self.extension_seqs = SequenceCollection.read(self.extension_seqs)
     result = _make_mini_otu_files(self.key_node,
                                   self.extension_genus_dic_few,
                                   self.extension_seqs)
     os.system("rm -r tmp")
     self.assertEqual(result, """>P1\nTTAAAAAA\n""")