def consensus_alignment(scoring_matrix, align_sequence):
'''
compute the similarity of the two sequences in the local alignment computed to
the PAX Domain.
global alignment of local align_x vs PAX Domain, local align_y vs PAX Domain
return the alignment and the persentage of elements in these two sequences that agree
'''
pax_domain = read_protein('ConsensusPAXDomain.txt')
align_sequence = align_sequence.replace("-", "")
alignment_matrix = compute_alignment_matrix(seq_x=align_sequence,
seq_y=pax_domain,
scoring_matrix=scoring_matrix,
global_flag=True)
score, global_align_sequence, global_align_pax = compute_global_alignment(
seq_x=align_sequence,
seq_y=pax_domain,
scoring_matrix=scoring_matrix,
alignment_matrix=alignment_matrix)
seq = difflib.SequenceMatcher(None, global_align_sequence,
global_align_pax)
ratio = seq.ratio()
#import pdb; pdb.set_trace()
return global_align_sequence, ratio
def get_edit_distance(seq_x, seq_y, scoring_matrix):
'''
compute the seq_x and seq_y global alignment with scoring matrix
return the edit distance can be expressed in term of:
|x| + |y| - score(x, y)
'''
alignment_matrix = compute_alignment_matrix(seq_x, seq_y, scoring_matrix, True)
score, align_x, align_y = compute_global_alignment(seq_x, seq_y, scoring_matrix, alignment_matrix)
return len(seq_x) + len(seq_y) - score
def get_edit_distance(seq_x, seq_y, scoring_matrix):
'''
compute the seq_x and seq_y global alignment with scoring matrix
return the edit distance can be expressed in term of:
|x| + |y| - score(x, y)
'''
alignment_matrix = compute_alignment_matrix(seq_x, seq_y, scoring_matrix,
True)
score, align_x, align_y = compute_global_alignment(seq_x, seq_y,
scoring_matrix,
alignment_matrix)
return len(seq_x) + len(seq_y) - score
def consensus_alignment(scoring_matrix, align_sequence):
'''
compute the similarity of the two sequences in the local alignment computed to
the PAX Domain.
global alignment of local align_x vs PAX Domain, local align_y vs PAX Domain
return the alignment and the persentage of elements in these two sequences that agree
'''
pax_domain = read_protein('ConsensusPAXDomain.txt')
align_sequence = align_sequence.replace("-", "")
alignment_matrix = compute_alignment_matrix(seq_x=align_sequence, seq_y=pax_domain, scoring_matrix=scoring_matrix, global_flag=True)
score, global_align_sequence, global_align_pax = compute_global_alignment(seq_x=align_sequence, seq_y=pax_domain, scoring_matrix=scoring_matrix, alignment_matrix=alignment_matrix)
seq = difflib.SequenceMatcher(None, global_align_sequence, global_align_pax)
ratio = seq.ratio()
#import pdb; pdb.set_trace()
return global_align_sequence, ratio
