else:
symbolCount[symbol] = 1
if ("-" in symbolCount) and symbolCount["-"] == len(column):
columnHomogeneity.append(0)
else:
upperTerm = 0
lowerTerm = 0
for symbol in symbolCount:
if symbol != "-":
upperTerm += pow(symbolCount[symbol], 2)
lowerTerm += symbolCount[symbol]
columnHomogeneity.append(upperTerm / pow(lowerTerm, 2))
allSymbolCounts.append(symbolCount)
# for sc,ch in zip(allSymbolCounts,columnHomogeneity):
# print(sc, ch)
return columnHomogeneity
if __name__ == "__main__":
filename = "../testfiles/mini-fasta-test.fst"
balign = cReadFASTA(filename)
calign = purgeColordal(columnifyBasal(balign))
print(calign)
columnHomogeneity = computeColumnHomogeneity(calign.columns)
print(columnHomogeneity)
print(sum(columnHomogeneity) / len(columnHomogeneity))
#columnHomogeneity = columneval.computeColumnHomogeneity(colordalign.columnifyBasal(basalPreIM).columns)
#print('Initial CH:', sum(columnHomogeneity)/len(columnHomogeneity))
sio = io.StringIO()
#basicalign.printFASTA(basalPreIM, sio)
tmpFile = open('/tmp/alintmp.fst','w')
basicalign.printFASTA(basalPreIM,tmpFile)
tmpFile.close()
process = subprocess.Popen(FFTNS, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = process.communicate( bytes(sio.getvalue(), 'utf-8') )
basalPostIM = basicalign.readFASTA( io.StringIO(out.decode()) )
colordal = colordalign.columnifyBasal(basalPostIM)
partitions = partitionalign.partitionAlignment(colordal, columneval.computeColumnHomogeneity, 0.85, 10)
partitionsPost = []
offset = 0
size = 0;
mutable_counter = 0;
for part,ann in partitions:
offset = offset + size
size = len(part)
#if ann:
if ann and size >= mlp:
mutable_counter = mutable_counter + 1
print("Mutable", offset, '-', offset+size-1, '('+str(size)+')', file=sys.stderr)
#print('Mutable partition:')
basalpartPre = partitionalign.basalifyPartition(part, colordal.names)
