def mult_align(sum_dict, align_dict):
"""Returns a biopython multiple alignment instance (MultipleSeqAlignment)"""
mult_align_dict = {}
for j in align_dict.abs(1).pos_align_dict:
mult_align_dict[j] = ''
for i in range(1, len(align_dict) + 1):
# loop on positions
for j in align_dict.abs(i).pos_align_dict:
# loop within a position
mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
alpha = Alphabet.Gapped(Alphabet.IUPAC.extended_protein)
fssp_align = MultipleSeqAlignment([], alphabet=alpha)
for i in sorted(mult_align_dict):
fssp_align.append(
SeqRecord(Seq(mult_align_dict[i], alpha),
sum_dict[i].pdb2 + sum_dict[i].chain2))
return fssp_align
def get_alphabet(self):
alph = self.alphabets.get(self.type, Alphabet.generic_alphabet)
if self.mol_seq and self.mol_seq.is_aligned:
return Alphabet.Gapped(alph)
return alph
print(consensus)
print("")
print(
summary.pos_specific_score_matrix(chars_to_ignore=['-'],
axis_seq=consensus))
print("")
#Have a generic alphabet, without a declared gap char, so must tell
#provide the frequencies and chars to ignore explicitly.
print(
summary.information_content(e_freq_table=expected,
chars_to_ignore=['-']))
print("")
print("Trying a protein sequence with gaps and stops")
alpha = Alphabet.HasStopCodon(
Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
a = Alignment(alpha)
a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")
a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")
a.add_sequence("ID003", "MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*")
print(a)
print("=" * a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
print(c)
c = s.gap_consensus(ambiguous="X")
print(c)
print("")
print(s.pos_specific_score_matrix(chars_to_ignore=['-', '*'], axis_seq=c))
