def run(self):
if not os.path.isdir(self.polishing_dir):
os.mkdir(self.polishing_dir)
prev_assembly = self.in_contigs
contig_lengths = None
for i in xrange(self.args.num_iters):
logger.info("Polishing genome ({0}/{1})".format(i + 1,
self.args.num_iters))
alignment_file = os.path.join(self.polishing_dir,
"minimap_{0}.sam".format(i + 1))
logger.info("Running Minimap2")
aln.make_alignment(prev_assembly, self.reads, self.args.threads,
self.polishing_dir, self.args.platform,
alignment_file)
logger.info("Separating alignment into bubbles")
contigs_info = aln.get_contigs_info(prev_assembly)
bubbles_file = os.path.join(self.polishing_dir,
"bubbles_{0}.fasta".format(i + 1))
coverage_stats = \
bbl.make_bubbles(alignment_file, contigs_info, prev_assembly,
self.args.platform, self.args.threads,
config.vals["min_aln_rate"], bubbles_file)
logger.info("Correcting bubbles")
polished_file = os.path.join(self.polishing_dir,
"polished_{0}.fasta".format(i + 1))
contig_lengths = pol.polish(bubbles_file, self.args.threads,
self.args.platform, self.polishing_dir,
i + 1, polished_file)
prev_assembly = polished_file
with open(self.out_files["stats"], "w") as f:
f.write("seq_name\tlength\tcoverage\n")
for ctg_id in contig_lengths:
f.write("{0}\t{1}\t{2}\n".format(ctg_id,
contig_lengths[ctg_id], coverage_stats[ctg_id]))
def test_paren(self):
self.assertEquals(polish.polish("(A + B) * C"), "AB+C*")
def test_mult_add(self):
self.assertEquals(polish.polish("A * B + C"), "AB*C+")
def test_add_mult(self):
self.assertEquals(polish.polish("A + B * C"), "ABC*+")
def test_simple_mult(self):
self.assertEquals(polish.polish("A * B"), "AB*")
def test_multi_addition(self):
self.assertEquals(polish.polish("A + B + C"), "ABC++")
def test_simple_addition(self):
self.assertEquals(polish.polish("A + B"), "AB+")
def test_paren(self):
self.assertEquals(polish.polish("(A + B) * C"), "AB+C*")
def test_add_mult(self):
self.assertEquals(polish.polish("A + B * C"), "ABC*+")
def test_mult_add(self):
self.assertEquals(polish.polish("A * B + C"), "AB*C+")
def test_simple_mult(self):
self.assertEquals(polish.polish("A * B"), "AB*")
def test_multi_addition(self):
self.assertEquals(polish.polish("A + B + C"), "ABC++")
def test_simple_addition(self):
self.assertEquals(polish.polish("A + B"), "AB+")
def test_complex(self):
self.assertEquals(polish.polish("(A + B) * (B + C * F)"), "AB+BCF*+*")
def test_complex(self):
self.assertEquals(polish.polish("(A + B) * (B + C * F)"), "AB+BCF*+*")
norm = e2.contract(AT[j], AT[lut[j, 0, 1]])
czz += e2.contract(ZT[j], ZT[lut[j, 0, 1]]) / norm
w1 = np.dot(e.c1[j], e.c2[lut[j, 1, 0]])
w2 = np.dot(e.c3[lut[j, 1, 1]], e.c4[lut[j, 0, 1]])
xi = np.linalg.svd(np.dot(w1, w2))[1]
xi = xi[np.nonzero(xi)]
S += np.dot(xi ** 2, np.log(xi))
E = (-czz - h * mx) / n
mz /= n
return [mz, S, E]
return test_fct_impl
a, nns = peps.load(basepath_in + statefile)
lut = util.build_lattice_lookup_table(nns, [4, 4])
def save_callback(a):
peps.save(a, lut, basepath_out + statefile[statefile.rfind("/") + 1 :])
ecf = tebd.CTMRGEnvContractorFactory(lut, chi, test_fct, 1e-12, 1e-15)
a = polish(a, lut, ecf, num_workers=num_workers, peps_save_callback=save_callback)
peps.save(a, lut, basepath_out + statefile[statefile.rfind("/") + 1 :])
print "tfi_gs_polish.py done; needed {0:f} seconds".format(time() - t0)
import lexems
from pars import *
import polish
if __name__ == '__main__':
file = open("test.txt")
text = file.read()
file.close()
tokens = lexems.lex(text)
for token in tokens:
print(token.element, token.type)
flag = if_right(tokens)
if flag:
print('true')
polish.polish(tokens)
