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Commit c9b7e8a9 authored by Rohmer Coralie's avatar Rohmer Coralie
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fix consensus majoritaire

parent 69d79b42
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......@@ -177,6 +177,7 @@ def majority_consensus(alignment):
if(letter_counter == max_counter):
max_letters.append(letter)
if ( len(max_letters) > 1):
max_letters.sort()
id_iupac = "".join((max_letters))
seq+=nuc_to_iupac[id_iupac]
else:
......@@ -184,33 +185,6 @@ def majority_consensus(alignment):
return seq
# max_frequency = 0
# max_letters=[]
# for letter in letters:
# pass
# frequency_letter=(len(re.findall(letter,nucleotides))/nb_reads)
# if max_frequency < frequency_letter:
# pass
# max_frequency = frequency_letter
# max_letters = [letter]
# else:
# if max_frequency==frequency_letter:
# pass
# max_letters = max_letters + [letter]
# if len(max_letters) <= 1:
# if max_letters[0] != '-':
# pass
# seq+=max_letters[0]
# else:
# max_letters.sort()
# id_iupac = "".join((max_letters))
# id_iupac = id_iupac.replace('-','')
# try:
# seq+=nuc_to_iupac[id_iupac]
# except:
# seq+="["+id_iupac+"]"
#Creation of the consensus sequence
def index_jaccard(nuc_ref,nuc_cons):
nb_nuc_ref = len(nuc_ref)
......
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