align_ngs_codons_tests.py

import unittest
from align_ngs_codons import pairwise_align_dna
from align_ngs_codons import gap_padding
from align_ngs_codons import translate_dna
from align_ngs_codons import get_cons_regions
from align_ngs_codons import get_var_regions


class MyTestCase(unittest.TestCase):

    reference_dna = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTG" \
                    "GGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATG" \
                    "TTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATG" \
                    "GTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAA" \
                    "TGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGG" \
                    "AAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAAT" \
                    "ACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAA" \
                    "TAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATG" \
                    "GTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAAT" \
                    "TGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGC" \
                    "ACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACT" \
                    "CATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTT" \
                    "AATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTA" \
                    "TGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCA" \
                    "GACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGA" \
                    "AGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATC" \
                    "AATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGC" \
                    "AACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCT" \
                    "GGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGA" \
                    "TAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACA" \
                    "GTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATA" \
                    "ATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCT" \
                    "CGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCC" \
                    "TGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACA" \
                    "GGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGC" \
                    "AGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAG" \
                    "CTTTGCTA"

    # test the prelim align function
    # @unittest.skip('Skip this test')
    def test_start_1_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_start_2_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_good_start_2": "TTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_good_start_2": "TTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_2": "TTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_start_3_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_good_start_3": "CTTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_good_start_3": "CTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_3": "CTTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_del_1_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_del_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_out = {"CAP255_2000_C1C3_del_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATT-GAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_del_2_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_del_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCAAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_out = {"CAP255_2000_C1C3_del_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCA-AATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_del_3_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_del_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        ref_out = {"CAP255_2000_C1C3_del_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        test_out = {"CAP255_2000_C1C3_del_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTG-ACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_del_2_or_3_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_del_2_or_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_out = {"CAP255_2000_C1C3_del_2_or_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del_2_or_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAA-TGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_1_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGG-AAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_2_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_ins_2": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_ins_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAA-GGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_2": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_3_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_ins_3": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_out = {"CAP255_2000_C1C3_ins_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTC-TTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_3": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # @unittest.skip('Skip this test')
    def test_del_large_pairwise_align_DNA(self):
        reference = "ATGACAGTGATGGGGATACAGAAGAATTACCAACAGTGGTGGATATGGGGAATCTTAGGCTTTTGGATGCTAATGATTTGTAATGGGAATGACACGTGGGTCACAGTATATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGAGAAAGAAGTGCATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATGGTTTTGGAAAATGTAACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGATCAGATGCATGAAGATATAATCAGTTTATGGGATCAAAGCCTCAAGCCATGTGTAAAGTTGACCCCGCTCTGTGTCACTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTTTGCGATTCTAAAGTGTAATAATAAGACATTCAATGGCACAGGACCATGCAATAATGTCAGCACAGTACAATGTACACATGGGATTAGGCCAGTGGTCTCAACTCAACTATTGTTAAATGGTAGCCTAGCAGAAAAAGAGATAATAATTAGATCTGAAAATCTGACAAACAATATCAAAACAATAATAGTACATCTCAATGAATCTGTAGAGATTAATTGTATAAGACCCAATAATAATACAAGGAAAAGTATGAGAATAGGACCAGGACAAACATTCTATGCAACAGGAGAAATAATAGGAGATATAAGGCAAGCACATTGTAACATTAGCAAAGATAAATGGGACAAAACTTTACACAGGGTAAGTGAAAAATTAAGAGAACACTTCCCTAATAAGACAATAACATTTAACTCATCCTCAGGAGGAGACCTAGAAATTACAACACATAGCTTTAATTGTGGAGGAGAATTTTTCTATTGCAATACATCAGGCCTGTTTAATAGTACATTTAATACTACATTTTATGAACCTTCAAATTTAACCATCACACTCCAATGCAGAATAAAACAAATTATAAACATGTGGCAGGAGGTGGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTGAATCAAAGATCACAGGGCTAATATTGACACGTGATGGAGGAAGTGACAATGGGACAGAGACATTCAGACCTGGAGGAGGAGATATGAGGGACAACTGGAGAAGTGAATTATATAAATATAAAGTGGTAGAAATTAAGCCATTGGGAATAGCACCCACTAATGGAAGAAGGAGAGTGGTGCAGAGAGAGAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCGGCATCAATAACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGGGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCTTGGCTCTAGAAAGATACCTAAGGGATCAACAGCTCCTAGGGATGTGGGGCTGCTCTGGAAAACTCATCTGCACCACTAATGTGGCTTGGAACTCTAGTTGGAGTAATAAAAGTCAAGATGAGATTTGGAAGAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTGACTATACAAACACAATATACAGGTTGCTTGAAGAGTCGCAAAACCAGCAAGAAATAAATGAAAAAGATTTACTAGCATTGGACAGTTGGAACAATCTGTGGACTTGGTTTGACATAACAAACTGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTGATAGGGTTAAGAATAATTTTTGCTGTGCTTTCTCTAGTGAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTGCAGACCTTTACCCCAAACCCGAGGGGACCCGACAGGCTCGAAAGAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGCGATTAGTGAGCGGATTCTTAGCACTTGCCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTATCACCTATTGAGAGACTTCATATTGGTTGCAGCGAGAGCAGTGGGACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAATATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTCTGCTTGATACCTTAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCATACAAAGAATTTGTAGAGCTATCCTCCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCTA"
        test_in = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGCACTTTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_out = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGCACT------------------TTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            seq_align, ref_align, frame = pairwise_align_dna(test_in[name], reference)
            self.assertEquals(seq_align, test_out[name])
            self.assertEquals(ref_align, ref_out[name])

    # test the gap padding function

    # @unittest.skip('Skip this test')
    def test_start_1_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_start_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_start_1"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])


    # @unittest.skip('Skip this test')
    def test_start_2_gap_padding(self):
        frame = 2
        test_in = {"CAP255_2000_C1C3_good_start_2": "TTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_start_2": "TTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_2": "--TTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_start_2"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])


    # @unittest.skip('Skip this test')
    def test_start_3_gap_padding(self):
        frame = 1
        test_in = {"CAP255_2000_C1C3_good_start_3": "CTTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_start_3": "CTTTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_3": "-CTTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_start_3"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_1_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATT-GAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_in = {"ref_del_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATT-GAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_del_1"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_2_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCA-AATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_in = {"ref_del_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCA-AATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_del_2"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_3_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTG-ACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        ref_in = {"ref_del_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        test_out = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTG-ACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTTT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_del_3"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_2_or_3_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAA-TGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_in = {"ref_del_2_or_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAA-TGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_del_2_or_3"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_1_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_ins_1": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGG-AAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAA--AAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_ins_1"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_2_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_ins_2": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_ins_2": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAA-GGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_2": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGG--GAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_ins_2"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_3_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_ins_3": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        ref_in = {"ref_ins_3": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAA---TAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTC-TTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_3": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCT--TTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_ins_3"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_large_gap_padding(self):
        frame = 0
        test_in = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGCACTTTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        ref_in = {"ref_large_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAACTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGCACTTTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        for name, seq in test_in.items():
            padded_sequence = gap_padding(seq, ref_in["ref_large_del"], frame, seq.replace("-", ""))
            self.assertEquals(padded_sequence, test_out[name])

    # test the translate function

    # @unittest.skip('Skip this test')
    def test_start_1_translate_dna(self):
        test_in = {"CAP255_2000_C1C3_good_start_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_1": "LNCSNASSNANVTKVDNSSTIGEIKNCTFNVTTELRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVX"}
        for name, seq in test_in.items():
            prot_seq = translate_dna(seq)
            self.assertEquals(prot_seq, test_out[name])

    # @unittest.skip('Skip this test')
    def test_start_2_translate_dna(self):
        test_in = {"CAP255_2000_C1C3_good_start_2": "--TTTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_good_start_2": "XLNCSNASSNANVTKVDNSSTIGEIKNCTFNVTTELRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVX"}
        for name, seq in test_in.items():
            prot_seq = translate_dna(seq)
            self.assertEquals(prot_seq, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_1_translate_dna(self):
        test_in = {"CAP255_2000_C1C3_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATT-GAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_del": "LNCSNANSNTNVTDIDNSTIXEIKNCTFNVTTELRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVSX"}
        for name, seq in test_in.items():
            prot_seq = translate_dna(seq)
            self.assertEquals(prot_seq, test_out[name])

    # @unittest.skip('Skip this test')
    def test_ins_1_translate_dna(self):
        test_in = {"CAP255_2000_C1C3_ins_1": "TTAAACTGTAGCAATGCAAGTAGCAATGCAAATGTCACAAAGGTTGATAATAGTAGCACAATTGGAGAAATAAAGAATTGCACTTTCAATGTAACTACAGAATTAAGAGATAAGGAAA--AAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTTAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCT"}
        test_out = {"CAP255_2000_C1C3_ins_1": "LNCSNASSNANVTKVDNSSTIGEIKNCTFNVTTELRDKEXKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVX"}
        for name, seq in test_in.items():
            prot_seq = translate_dna(seq)
            self.assertEquals(prot_seq, test_out[name])

    # @unittest.skip('Skip this test')
    def test_del_large_translate_dna(self):
        test_in = {"CAP255_2000_C1C3_good_del": "TTAAACTGTAGCAATGCAAATAGCAATACAAATGTCACAGATATTGATAATAGCACAATTGGAGAAATAAAGAATTGCACTTTAAGAGATAAGGAAAAGAAAGAAAATGCACTCTTTTATAAACTTGATATAGTACCACTTAATGGAAATAACAACAGCAGCTTCAGTATGTATAGATTAATAAACTGTAATACCTCAGTCGTAACACAAGCCTGTCCAAAGGTCTCTTT"}
        test_out = {"CAP255_2000_C1C3_good_del": "LNCSNANSNTNVTDIDNSTIGEIKNCTLRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVSX"}
        for name, seq in test_in.items():
            prot_seq = translate_dna(seq)
            self.assertEquals(prot_seq, test_out[name])

    # test the find conserved and variable regions function
    # @unittest.skip('Skip this test')
    def test_find_cons_regions(self):
        test_in = {
            "full_env": "MTVMGIQKNYQQWWIWGILGFWMLMICNGNDTWVTVYYGVPVWREAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSNANSNTNVTDIDNSTIGEIKNCTFNVTTELRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVSFDPIPIHYCAPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIIIRSENLTNNIKTIIVHLNESVEINCIRPNNNTRKSMRIGPGQTFYATGEIIGDIRQAHCNISKDKWDKTLHRVSEKLREHFPNKTITFNSSSGGDLEITTHSFNCGGEFFYCNTSGLFNSTFNTTFYEPSNLTITLQCRIKQIINMWQEVGRAMYAPPIAGNITCESKITGLILTRDGGSDNGTETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTNGRRRVVQREKRAVGIGAVFLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQNNLLRAIEAQQHMLQLTVWGIKQLQARVLALERYLRDQQLLGMWGCSGKLICTTNVAWNSSWSNKSQDEIWKNMTWMQWDREISDYTNTIYRLLEESQNQQEINEKDLLALDSWNNLWTWFDITNWLWYIKIFIMIVGGLIGLRIIFAVLSLVNRVRQGYSPLSLQTFTPNPRGPDRLERIEEEGGEQDRDRSVRLVSGFLALAWDDLRSLCLFSYHLLRDFILVAARAVGLLGRSSLRGLQTGWEALKYLGSLVQYWGLELKKSAISLLDTLAIAVAEGTDRIIEFIQRICRAILHIPRRIRQGFEAALL"}

        test_out = {'C1': 'MRVMGIQRNCPQWWIWGILGFWMLMICSVVGKLWVTVYYGVPVWREAKTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNDMVDQMHEDIISLWDESLKPCVKLTPLCVTLNCVNANRTINVTTTG',
                    'C2': 'EIKNCSFNVTTELRDKERKEYALFYRLDIVPLNNESSSDDTEYRLINCNTSAIKQACPKVSFDPIPIHYCAPAGFAILKCNNNTFNGTGPCTNVSTVQCTHGIKPVMSTQLLLNGSLAEGEIIIRSENLTDNAKTIIVQLDKSVEITCTRPNNNTRKSVRIGPGQTFYATGDIIGNIRQAHCNISSNEWNNTLEKVKKRLKEHFPDKNITFAPSSGGDLEIATHSFNCRGEFF',
                    'C3': 'SNSTITLQCKIKQIIRMWQKVGQAMYAPPIAGNITCKSNITGLLLTRDGGR',
                    'C4': 'IFRPGGGNMRDNWRSELYKYKVVEIKPLGIAPTNAKRRVVEREKRAVGIGAVFLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIKQLQTRVLALERFLRDQQLLGLWGCSGKLICTTAVPWNSSWSNKSQDDIWHNMTWMQWDREINNYTGTIYRLLEESQSQQERNEKDLLALDSWNSLWNWFDITKWLWYIKLFIMIVGGLIGLRIIFAVLSIVKRVRQGYSPLSFQTLTPNPREPDRPGRIEEEGGEQDRDRSIRLVSGFLALIWDDLRSLCLFSYHQLRNFILVTARAVELLGRNSLRGLQRGWEALKYLGNLVLYWGLEIKKSAISLLDTIAIAVAEGTDRIIELIQRICRAIRNLPRRIRQGFEASLL'
                    }

        for name, seq in test_in.items():
            cons_d = get_cons_regions(test_out, 'C', 'C4')
            for k, v in cons_d.items():
                print(k)
                self.assertEquals(v, test_out[k])

# test the find conserved and variable regions function
    @unittest.skip('Skip this test')
    def test_find_var_regions(self):
        test_in = {"full_env": "MTVMGIQKNYQQWWIWGILGFWMLMICNGNDTWVTVYYGVPVWREAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSNANSNTNVTDIDNSTIGEIKNCTFNVTTELRDKEKKENALFYKLDIVPLNGNNNSSFSMYRLINCNTSVVTQACPKVSFDPIPIHYCAPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIIIRSENLTNNIKTIIVHLNESVEINCIRPNNNTRKSMRIGPGQTFYATGEIIGDIRQAHCNISKDKWDKTLHRVSEKLREHFPNKTITFNSSSGGDLEITTHSFNCGGEFFYCNTSGLFNSTFNTTFYEPSNLTITLQCRIKQIINMWQEVGRAMYAPPIAGNITCESKITGLILTRDGGSDNGTETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTNGRRRVVQREKRAVGIGAVFLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQNNLLRAIEAQQHMLQLTVWGIKQLQARVLALERYLRDQQLLGMWGCSGKLICTTNVAWNSSWSNKSQDEIWKNMTWMQWDREISDYTNTIYRLLEESQNQQEINEKDLLALDSWNNLWTWFDITNWLWYIKIFIMIVGGLIGLRIIFAVLSLVNRVRQGYSPLSLQTFTPNPRGPDRLERIEEEGGEQDRDRSVRLVSGFLALAWDDLRSLCLFSYHLLRDFILVAARAVGLLGRSSLRGLQTGWEALKYLGSLVQYWGLELKKSAISLLDTLAIAVAEGTDRIIEFIQRICRAILHIPRRIRQGFEAALL"}

        test_out = {'V1': 'SNTNVTDIDNSTI',
                    'V2': 'TFNTTFYE',
                    'V3': 'SDNGTE'
                    }
        for name, seq in test_in.items():
            var_d = get_var_regions(seq)
            for k, v in var_d.items():
                print(k)
                self.assertEquals(v, test_out[k])



if __name__ == '__main__':
    unittest.main()