else:
result = minimize(f,
x0,
bounds=bounds,
args=(tree, seqs),
method='SLSQP',
options={'maxiter': maxit})
x = result.x
pi = {'A': x[0], 'C': x[1], 'G': x[2], 'T': (1 - x[0] - x[1] - x[2])}
gtr = {
'AC': x[3],
'AG': x[4],
'AT': x[5],
'CG': x[6],
'CT': x[7],
'GT': x[8]
}
return pi, gtr
# main function
if __name__ == "__main__":
args = parseArgs()
tree = dendropy.Tree.get(file=args.tree, schema='newick')
seqs = parseFASTA(args.seqs)
pi, R = MLGTR(tree, seqs, maxit=args.maxit)
args.out.write(' '.join([str(pi[c]) for c in 'ACGT']) + '\n')
args.out.write(
str(R['CT']) + ' ' + str(R['AT']) + ' ' + str(R['GT']) + ' ' +
str(R['AC']) + ' ' + str(R['CG']) + ' ' + str(R['AG']) + '\n')
help="Input FASTA File")
parser.add_argument('-o',
'--output',
required=False,
type=argparse.FileType('w'),
default=sys.stdout,
help="Output FASTA File")
parser.add_argument('-p',
'--indel',
required=False,
type=float,
default=0.1,
help="Indel Ratio")
args = parser.parse_args()
start_time = time.time()
sys.stderr.write("User-specified indel rate: " + str(args.indel) + '\n')
gap = indelToGap(args.indel)
sys.stderr.write("Indel rate converted to gap rate: " + str(gap) + '\n')
sys.stderr.write("Parsing input FASTA file...\n")
seqs = parseFASTA(args.input)
sys.stderr.write("Computing 2D dynamic programming matrix...\n")
score, aln = pairAlign(seqs, gap)
sys.stderr.write("Writing output alignment...\n")
for ID in sorted(aln.keys()):
args.output.write('>')
args.output.write(ID)
args.output.write('\n')
args.output.write(aln[ID])
args.output.write('\n')
sys.stderr.write("--- Completed in %s seconds ---" %
(time.time() - start_time) + '\n')