raw_consensus = consensus.raw_consensus

alignments = msa.get_alignments()

contributions = {}

for name in list(alignments.keys()):

alignment = alignments[name]

contributions[name] = 1/len(alignment.replace('-',''))

current_var_sum = 0

variability_sums = []

conservation = []

## Calculate conservation at and variability before each character

# Go through each position in the alignment (based on the composite or gapped consensus)

for position in range(len(msa.composite)):

# If the current position is a gap, add contributions to the current variability sum

if raw_consensus[position] == '-':

# Go through each alignment to check whether it has a character at the current position

for name in list(alignments.keys()):

alignment = alignments[name]

# If it does have a character (not a gap '-'), add its variability contribution

if not alignment[position] == '-':

current_var_sum += contributions[name]

# The current position is a consensus character, so store the variability sum preceeding it

else:

# if the position within the ungapped consensus is needed, just use the current length of variability_sums

variability_sums.append(current_var_sum)

current_var_sum = 0

# determine the current position's conservation level

conservation_sum = 0

for alignment in list(alignments.values()):

# If it does have a character (not a gap '-'), add its conservation contribution

if not alignment[position] == '-':

conservation_sum += 1

conservation.append(conservation_sum/len(alignments))

newick_string = ""

cons_str = consensus.consensus

conservation,variability = calculate_conservation(msa,consensus)

a_stack = [(1,0)]

print(cons_str)

for position in range(len(cons_str)):

#print(str(position)+' '+cons_str[position])

#print(str(a_stack))

if cons_str[position] == 'A':

a_stack.append((0,0))

node_string = ')'

elif cons_str[position] == 'C':

node_string = ',:1)'

a_val = a_stack.pop()

a_stack.append((a_val[0],a_val[1]+1))

elif cons_str[position] == 'T':

node_string = '(:1,:1)'

not_done = 1

while not_done and len(a_stack) > 0:

a_val = a_stack.pop()

if a_val[0] == 0:

node_string = ','+a_val[1]*'('+node_string

a_stack.append((1,1))

not_done = 0

else:

node_string = a_val[1]*'('+node_string

newick_string = node_string + cons_str[position] + '-' + str(round(conservation[position],3)) + ':' + str(round(variability[position],3)) + newick_string

newick_string += ';'

status_message('Generating newick string','OK')

handle = open(args['newick'],'w')

handle.write(newick_string)

handle.close()

score_by_threshold = msa.score_by_threshold()

percent_cols_conserved = msa.percent_columns_conserved_by_threshold()

handle = open(args['scores'],'w')

for i in range(len(score_by_threshold)):

handle.write("%.3f,%.3f,%.3f\n" % (score_by_threshold[i][0],score_by_threshold[i][1],percent_cols_conserved[i][1]))

#print("%.3f %.3f %.3f" % (score_by_threshold[i][0],score_by_threshold[i][1],percent_cols_conserved[i][1]))

handle.close()