def test():
seq1 = "MGTSADNALAESFNSALKREVLQDRKVFDNHLVCRREVFYWCTRYNTHRLHTWCGYLSPDDYEAAA" # https://www.uniprot.org/uniprot/W5Y845.fasta
seq2 = "MLQTPCPQSGVRVPLAESFNSALKREVLQDRKVFDNHLVCRREVFYWCTRYNTHRLHTWCGYLSPDDYEAAA" # https://www.uniprot.org/uniprot/W5Y176.fasta
seq3 = "MKREVLQDAACWPDEATCRRQVFRWAVRYNTRRRHSWCGYLSPSTYEARWAATLPTAA" # https://www.uniprot.org/uniprot/A0A345NSW8.fasta
seq4 = "MLKREVLRDRKVFGNPIACRQEVFRWCMRYNTHRRHSWCNLVAPDVFETETSATLTKAT" # https://www.uniprot.org/uniprot/A0A127NSH0.fasta
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_score=-1,
gap_start=-1)
(line1, line2), score = align(seq4,
seq3,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_score=-1,
gap_start=-10)
(line1, line2), score = align(seq4,
seq3,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
(line1, line2), score = edit_distance(seq3, seq4, reconstruct_answer=True)
print(line1)
print(line2)
print(score)
def local_alignment_sample():
seq1 = "ACC"
seq2 = "AACCC"
#seq1 = "ALAESFNSALKQTPCPQSGVRVPLREVLQDRKVFDNHLVCYEAAA"
#seq2 = "MLQTPCPQSGVRVPLAESFNSALKREVLQDRKVFDNHLVCRREVFYWCTRYNTHRLHTWCGYLSPDDYEAAA" # https://www.uniprot.org/uniprot/W5Y176.fasta
method = alignments.NeedlemanWunsch(match_score=3,
mismatch_score=-3,
gap_score=-2)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
method = alignments.SmithWaterman(match_score=1,
mismatch_score=-1,
gap_score=-1)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
seq1 = "TGTTACGG"
seq2 = "GGTTGACTA"
method = alignments.SmithWaterman(match_score=1,
mismatch_score=-1,
gap_score=-1)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
def affine_gap_needleman_wunsch_sample():
seq1 = "TCCCAGTTATGTCAGGGGACACGAGCATGCAGAGAC"
seq2 = "AATTGCCGCCGTCGTTTTCAGCAGTTATGTCAGATC"
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_start=0,
gap_score=-1)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_start=-100,
gap_score=-0.01)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_start=0.5,
gap_score=-0.3)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
def simple_needleman_wunsch_sample():
seq1 = "MGTSADNALAESFNSALKREVLQDRKVFDNHLVCRREVFYWCTRYNTHRLHTWCGYLSPDDYEAAA"
seq2 = "MLQTPCPQSGVRVPLAESFNSALKREVLQDRKVFDNHLVCRREVFYWCTRYNTHRLHTWCGYLSPD"
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_score=-1)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
method = alignments.NeedlemanWunsch(match_score=1,
mismatch_score=-1,
gap_score=-0.499)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
def distance_matrix_sample():
seq1 = "XXXYZ"
seq2 = "ЙYXXX"
dist_matrix = {
'X': {
'-': -3,
'Й': -5,
'Z': -5,
'Y': -5,
'X': 5
},
'Y': {
'-': -5,
'Й': -5,
'Z': -5,
'Y': 5,
'X': -5
},
'Z': {
'-': 3,
'Й': -15,
'Z': 8,
'Y': -5,
'X': -5
},
'Й': {
'-': -3,
'Й': 8,
'Z': -15,
'Y': -5,
'X': -5
},
'-': {
'-': 0,
'Й': -3,
'Z': 3,
'Y': -5,
'X': -3
}
}
method = alignments.NeedlemanWunsch(score_matrix=dist_matrix)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
dist_matrix = {
'X': {
'-': 33,
'Й': -5,
'Z': -5,
'Y': -5,
'X': 5
},
'Y': {
'-': -5,
'Й': -5,
'Z': -5,
'Y': 5,
'X': -5
},
'Z': {
'-': 3,
'Й': -15,
'Z': 8,
'Y': -5,
'X': -5
},
'Й': {
'-': -3,
'Й': 8,
'Z': -15,
'Y': -5,
'X': -5
},
'-': {
'-': 0,
'Й': -3,
'Z': 3,
'Y': -5,
'X': 33
}
}
method = alignments.NeedlemanWunsch(score_matrix=dist_matrix)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)
dist_matrix = {
'X': {
'-': -3,
'Й': -5,
'Z': -5,
'Y': -5,
'X': 5
},
'Y': {
'-': -5,
'Й': -5,
'Z': -5,
'Y': 5,
'X': -5
},
'Z': {
'-': 3,
'Й': -15,
'Z': 8,
'Y': -5,
'X': -5
},
'Й': {
'-': -3,
'Й': 8,
'Z': -15,
'Y': -5,
'X': -5
},
'-': {
'-': 0,
'Й': -3,
'Z': 3,
'Y': -5,
'X': -3
}
}
method = alignments.NeedlemanWunsch(score_matrix=dist_matrix, gap_start=55)
(line1, line2), score = align(seq1,
seq2,
reconstruct_answer=True,
method=method)
print(line1)
print(line2)
print(score)