Align inputs and get mayority vote

align_and_fix.py

# Import pairwise2 module
from Bio import pairwise2

# Import format_alignment method
from Bio.pairwise2 import format_alignment

import itertools
import glob
from scipy import stats as s

def get(list, index, default):
  try:
    return list[index]
  except IndexError:
    return default

def align(X, Y):
  return pairwise2.align.globalms(X, Y, 1, 0, -1, -0.5)


def multi_align(seqs):
  scores = {k:0 for k in seqs}

  for X, Y in itertools.combinations(seqs, 2):
    alignments = align(X, Y)
    if len(alignments) == 0:
      score = 0
    else:
      score = alignments[0].score
    scores[X] += score
    scores[Y] += score

  sorted_seqs = [s for s in reversed(sorted(scores, key=scores.get))]

  main = None
  # Chequear que no loopee aca
  while (main != sorted_seqs[0]):
    main = sorted_seqs[0]
    for i in range(1, len(sorted_seqs)):
      X = sorted_seqs[0]

      Y = sorted_seqs[i]
      alignments = align(X, Y)

      max_score = 0
      best_align = None
      for a in alignments:
        if a.score > max_score:
          max_score = a.score
          best_align = a
      
        sorted_seqs[0] = a.seqA
        sorted_seqs[i] = a.seqB
  
  return sorted_seqs

files = []

for filepath in glob.iglob(r'input/*.txt'):
  f = open(filepath, "r")
  files.append(f.readlines())

maxlines = max([len(lines) for lines in files])
for line in range(maxlines):
  lines = [ get(f, line, '').strip() for f in files]
  while '' in lines:
    lines.remove('')
  aligned = multi_align(lines)

  #_ = [print(l) for l in aligned]

  clean = ''
  for i in range(len(aligned[0])):
    clean += s.mode( [get(seq,i,'-') for seq in aligned] ).mode[0]
  #print("-"*79)
  print(clean.replace('-',''))
  #print("")