def test_longer(self):
al = bs.alignment()
seq1 = 'CNNITDVDPCVFCSSPTRNQRLVCVVEEPTNIAAVEKTRGYNGVYHVLHGTLSPLHGVGPEHLRTVNLLARVERGEVDELILATSPTVEGEATANYLADLLRPLRVRLTRIATGVPAGSDIEYVDEVTMTRALEGRREL'
seq2 = 'MADVPSMDALVALLRRLPGIGPRSAQRISYELLVRKRDLMPQLAAAFQQAHAVVRFCERCNNLSEAPLCAVCRSEHRDRSILCVVESPADLRAIEDTGVFVGEFFVLMGHLSPLDGIGPEALHIDRLSARLGETDLQEVIFATNPTLEGEATAQFLAGLVPDGVTISRIARGVPVGGELEYVDRSTLGRALHGRRLLDE'
global_n_expected = 5760
self.assertEqual(
len(al.run_global_align_multiple_solutions(seq1, seq2, -3)),
global_n_expected)
local_expected = [
[
'CNNITDVDP_CVFCSSPTRNQRLVCVVEEPTNIAAVEKTRG_YNGVYHVLHGTLSPLHGVGPEHLRTVNLL_ARVERGEVD__ELILATSPTVEGEATANYLADLLRPLRVRLTRIATGVPAGSDIEYVDEVTMTRALEGRREL',
'CNNLSEA_PLCAVCRSEHRDRSILCVVESPADLRAIEDT_GVFVGEFFVLMGHLSPLDGIGPEALH_IDRLSARL__GETDLQEVIFATNPTLEGEATAQFLAGLV_PDGVTISRIARGVPVGGELEYVDRSTLGRALHGRRLL'
],
[
'CNNITDVDP_CVFCSSPTRNQRLVCVVEEPTNIAAVEKTRG_YNGVYHVLHGTLSPLHGVGPEHLRTVN_LLARVERGEVD__ELILATSPTVEGEATANYLADLLRPLRVRLTRIATGVPAGSDIEYVDEVTMTRALEGRREL',
'CNNLSEA_PLCAVCRSEHRDRSILCVVESPADLRAIEDT_GVFVGEFFVLMGHLSPLDGIGPEALH_IDRLSARL__GETDLQEVIFATNPTLEGEATAQFLAGLV_PDGVTISRIARGVPVGGELEYVDRSTLGRALHGRRLL'
],
[
'CNNITDVDP_CVFCSSPTRNQRLVCVVEEPTNIAAVEKTRG_YNGVYHVLHGTLSPLHGVGPEHLRTVNLL_ARVERGEVD__ELILATSPTVEGEATANYLADLLRPLRVRLTRIATGVPAGSDIEYVDEVTMTRALEGRREL',
'CNNLSEA_PLCAVCRSEHRDRSILCVVESPADLRAIEDT_GVFVGEFFVLMGHLSPLDGIGPEALH_IDRLSARL__GETDLQEVIFATNPTLEGEATAQFLAGLV_PDGVTISRIARGVPVGGELEYVDRSTLGRALHGRR_L'
],
[
'CNNITDVDP_CVFCSSPTRNQRLVCVVEEPTNIAAVEKTRG_YNGVYHVLHGTLSPLHGVGPEHLRTVN_LLARVERGEVD__ELILATSPTVEGEATANYLADLLRPLRVRLTRIATGVPAGSDIEYVDEVTMTRALEGRREL',
'CNNLSEA_PLCAVCRSEHRDRSILCVVESPADLRAIEDT_GVFVGEFFVLMGHLSPLDGIGPEALH_IDRLSARL__GETDLQEVIFATNPTLEGEATAQFLAGLV_PDGVTISRIARGVPVGGELEYVDRSTLGRALHGRR_L'
]
]
self.assertListEqual(
al.run_local_align_multiple_solutions(seq1, seq2, -3),
local_expected)
def test_recover_global_align_multiple_solutions(self):
al = bs.alignment()
(s, t) = al.global_align_multiple_solutions('PHSWG', 'HGWAG', -8)
expected = [['PHSW_G', '_HGWAG']]
self.assertListEqual(
al.recover_global_align_multiple_solutions('PHSWG', 'HGWAG', t,
-3), expected)
def test_c2(self):
sm = bs.alignment.create_substitution_matrix('ATCG', 1, -1)
al = bs.alignment(sm)
seq1 = 'GATTACA'
seq2 = 'GCATGCT'
al.run_global_align_multiple_solutions(seq1, seq2, -1)
al.run_local_align_multiple_solutions(seq1, seq2, -1)
def __init__(self, seqs, sm=False):
self.seqs = seqs
self.alignment = alignment(sm)
self.clusters = [str(i) for i, _ in enumerate(seqs)]
self.trees = {str(i): Tree(seq) for i, seq in enumerate(seqs)}
self.dist = self._calculate_distances()
self.original_dist = list(self.dist)
def __init__(self, seqs, sm=False, g=-3, species=False):
self.seqs = seqs # list of BioSeq objects
self.alignment = alignment(sm) # an Alignment instance
self.g = g
self.species = []
if species:
self.species = [s.species for s in self.seqs]
def test_global_align_multiple_solutions(self):
al = bs.alignment()
(s, t) = al.global_align_multiple_solutions('TACT', 'ACTA', -3)
self.assertListEqual(
s, [[0, -3, -6, -9, -12], [-3, 0, -3, -1, -4], [-6, 1, 0, -3, 3],
[-9, -2, 10, 7, 4], [-12, -5, 7, 15, 12]])
self.assertListEqual(
t, [[[3], [3], [3], [3], [3]], [[2], [1], [3], [1], [3]],
[[2], [1], [1], [1, 3], [1]], [[2], [2], [1], [3], [3]],
[[2], [2], [2], [1], [3]]])
def test_sm_constructor(self):
sm = bs.alignment.create_substitution_matrix('ATCG', 3, -1)
alignment = bs.alignment(sm)
self.assertDictEqual(
alignment.sm, {
'AA': 3,
'AT': -1,
'AC': -1,
'AG': -1,
'TA': -1,
'TT': 3,
'TC': -1,
'TG': -1,
'CA': -1,
'CT': -1,
'CC': 3,
'CG': -1,
'GA': -1,
'GT': -1,
'GC': -1,
'GG': 3
})
def test_default_constructor(self):
alignment = bs.alignment()
expected = {
'AA': 4,
'AR': -1,
'AN': -2,
'AD': -2,
'AC': 0,
'AQ': -1,
'AE': -1,
'AG': 0,
'AH': -2,
'AI': -1,
'AL': -1,
'AK': -1,
'AM': -1,
'AF': -2,
'AP': -1,
'AS': 1,
'AT': 0,
'AW': -3,
'AY': -2,
'AV': 0,
'RA': -1,
'RR': 5,
'RN': 0,
'RD': -2,
'RC': -3,
'RQ': 1,
'RE': 0,
'RG': -2,
'RH': 0,
'RI': -3,
'RL': -2,
'RK': 2,
'RM': -1,
'RF': -3,
'RP': -2,
'RS': -1,
'RT': -1,
'RW': -3,
'RY': -2,
'RV': -3,
'NA': -2,
'NR': 0,
'NN': 6,
'ND': 1,
'NC': -3,
'NQ': 0,
'NE': 0,
'NG': 0,
'NH': 1,
'NI': -3,
'NL': -3,
'NK': 0,
'NM': -2,
'NF': -3,
'NP': -2,
'NS': 1,
'NT': 0,
'NW': -4,
'NY': -2,
'NV': -3,
'DA': -2,
'DR': -2,
'DN': 1,
'DD': 6,
'DC': -3,
'DQ': 0,
'DE': 2,
'DG': -1,
'DH': -1,
'DI': -3,
'DL': -4,
'DK': -1,
'DM': -3,
'DF': -3,
'DP': -1,
'DS': 0,
'DT': -1,
'DW': -4,
'DY': -3,
'DV': -3,
'CA': 0,
'CR': -3,
'CN': -3,
'CD': -3,
'CC': 9,
'CQ': -3,
'CE': -4,
'CG': -3,
'CH': -3,
'CI': -1,
'CL': -1,
'CK': -3,
'CM': -1,
'CF': -2,
'CP': -3,
'CS': -1,
'CT': -1,
'CW': -2,
'CY': -2,
'CV': -1,
'QA': -1,
'QR': 1,
'QN': 0,
'QD': 0,
'QC': -3,
'QQ': 5,
'QE': 2,
'QG': -2,
'QH': 0,
'QI': -3,
'QL': -2,
'QK': 1,
'QM': 0,
'QF': -3,
'QP': -1,
'QS': 0,
'QT': -1,
'QW': -2,
'QY': -1,
'QV': -2,
'EA': -1,
'ER': 0,
'EN': 0,
'ED': 2,
'EC': -4,
'EQ': 2,
'EE': 5,
'EG': -2,
'EH': 0,
'EI': -3,
'EL': -3,
'EK': 1,
'EM': -2,
'EF': -3,
'EP': -1,
'ES': 0,
'ET': -1,
'EW': -3,
'EY': -2,
'EV': -2,
'GA': 0,
'GR': -2,
'GN': 0,
'GD': -1,
'GC': -3,
'GQ': -2,
'GE': -2,
'GG': 6,
'GH': -2,
'GI': -4,
'GL': -4,
'GK': -2,
'GM': -3,
'GF': -3,
'GP': -2,
'GS': 0,
'GT': -2,
'GW': -2,
'GY': -3,
'GV': -3,
'HA': -2,
'HR': 0,
'HN': 1,
'HD': -1,
'HC': -3,
'HQ': 0,
'HE': 0,
'HG': -2,
'HH': 8,
'HI': -3,
'HL': -3,
'HK': -1,
'HM': -2,
'HF': -1,
'HP': -2,
'HS': -1,
'HT': -2,
'HW': -2,
'HY': 2,
'HV': -3,
'IA': -1,
'IR': -3,
'IN': -3,
'ID': -3,
'IC': -1,
'IQ': -3,
'IE': -3,
'IG': -4,
'IH': -3,
'II': 4,
'IL': 2,
'IK': -3,
'IM': 1,
'IF': 0,
'IP': -3,
'IS': -2,
'IT': -1,
'IW': -3,
'IY': -1,
'IV': 3,
'LA': -1,
'LR': -2,
'LN': -3,
'LD': -4,
'LC': -1,
'LQ': -2,
'LE': -3,
'LG': -4,
'LH': -3,
'LI': 2,
'LL': 4,
'LK': -2,
'LM': 2,
'LF': 0,
'LP': -3,
'LS': -2,
'LT': -1,
'LW': -2,
'LY': -1,
'LV': 1,
'KA': -1,
'KR': 2,
'KN': 0,
'KD': -1,
'KC': -3,
'KQ': 1,
'KE': 1,
'KG': -2,
'KH': -1,
'KI': -3,
'KL': -2,
'KK': 5,
'KM': -1,
'KF': -3,
'KP': -1,
'KS': 0,
'KT': -1,
'KW': -3,
'KY': -2,
'KV': -2,
'MA': -1,
'MR': -1,
'MN': -2,
'MD': -3,
'MC': -1,
'MQ': 0,
'ME': -2,
'MG': -3,
'MH': -2,
'MI': 1,
'ML': 2,
'MK': -1,
'MM': 5,
'MF': 0,
'MP': -2,
'MS': -1,
'MT': -1,
'MW': -1,
'MY': -1,
'MV': 1,
'FA': -2,
'FR': -3,
'FN': -3,
'FD': -3,
'FC': -2,
'FQ': -3,
'FE': -3,
'FG': -3,
'FH': -1,
'FI': 0,
'FL': 0,
'FK': -3,
'FM': 0,
'FF': 6,
'FP': -4,
'FS': -2,
'FT': -2,
'FW': 1,
'FY': 3,
'FV': -1,
'PA': -1,
'PR': -2,
'PN': -2,
'PD': -1,
'PC': -3,
'PQ': -1,
'PE': -1,
'PG': -2,
'PH': -2,
'PI': -3,
'PL': -3,
'PK': -1,
'PM': -2,
'PF': -4,
'PP': 7,
'PS': -1,
'PT': -1,
'PW': -4,
'PY': -3,
'PV': -2,
'SA': 1,
'SR': -1,
'SN': 1,
'SD': 0,
'SC': -1,
'SQ': 0,
'SE': 0,
'SG': 0,
'SH': -1,
'SI': -2,
'SL': -2,
'SK': 0,
'SM': -1,
'SF': -2,
'SP': -1,
'SS': 4,
'ST': 1,
'SW': -3,
'SY': -2,
'SV': -2,
'TA': 0,
'TR': -1,
'TN': 0,
'TD': -1,
'TC': -1,
'TQ': -1,
'TE': -1,
'TG': -2,
'TH': -2,
'TI': -1,
'TL': -1,
'TK': -1,
'TM': -1,
'TF': -2,
'TP': -1,
'TS': 1,
'TT': 5,
'TW': -2,
'TY': -2,
'TV': 0,
'WA': -3,
'WR': -3,
'WN': -4,
'WD': -4,
'WC': -2,
'WQ': -2,
'WE': -3,
'WG': -2,
'WH': -2,
'WI': -3,
'WL': -2,
'WK': -3,
'WM': -1,
'WF': 1,
'WP': -4,
'WS': -3,
'WT': -2,
'WW': 11,
'WY': 2,
'WV': -3,
'YA': -2,
'YR': -2,
'YN': -2,
'YD': -3,
'YC': -2,
'YQ': -1,
'YE': -2,
'YG': -3,
'YH': 2,
'YI': -1,
'YL': -1,
'YK': -2,
'YM': -1,
'YF': 3,
'YP': -3,
'YS': -2,
'YT': -2,
'YW': 2,
'YY': 7,
'YV': -1,
'VA': 0,
'VR': -3,
'VN': -3,
'VD': -3,
'VC': -1,
'VQ': -2,
'VE': -2,
'VG': -3,
'VH': -3,
'VI': 3,
'VL': 1,
'VK': -2,
'VM': 1,
'VF': -1,
'VP': -2,
'VS': -2,
'VT': 0,
'VW': -3,
'VY': -1,
'VV': 4
}
self.assertDictEqual(alignment.sm, expected)
def test_local_align_multiple_solutions(self):
sm = bs.alignment.create_substitution_matrix('ANDR', 3, -1)
al = bs.alignment(sm)
seq1 = 'ANDDR'
seq2 = 'AARRD'
al.run_local_align_multiple_solutions(seq1, seq2, -8)