def test_rebuild_sequence(self):
pass
#give a sequence
seq_given = "ATGTGTGCCCTTGAAACCCC"
# here we build fake snp file
tmp_file_name = "./fake_snp.rnasnp"
tmp_file_with_line = "./snp_line.rnasnp"
table_head = "SNP w Slen GC interval d pvalue1 ewin interval d_max pvalue2"
describe_line_one = "200 2463 0.5373 1-26 0.0361 0.0943 200 1-53 0.0072 0.4643"
snp_line_picked_out = "200 2463 0.5373 1-26 0.0361 0.0943 200 1-53 0.0072 0.0643"
p2_less = 0.0643
line_num_pick = 9
with open(tmp_file_name, "w") as snp_faker:
snp_faker.write(table_head)
snps = []
for index_nt, nt in enumerate(seq_given):
snps.extend(RNAsnp.mutation_one_site(nt, index_nt + 1))
snp_faker.write("\n".join(snps))
with open(tmp_file_with_line, "w") as snps_add_line:
snps_add_line.write(table_head)
snp_lines = []
for snp in snps:
if snps.index(snp) == line_num_pick:
snp_lines.append("\t".join([snp, snp_line_picked_out]))
else:
snp_lines.append("\t".join([snp, describe_line_one]))
snps_add_line.writelines("\n".join(snp_lines))
# use this file as input for pyRNAsnp.get_snp_list.
rebuilded_seq = RNAsnp.rebuild_seq(tmp_file_name)
self.assertEqual(seq_given, rebuilded_seq)
# test how to pick out a line with less p-value
picked_collected = []
with open(tmp_file_with_line, "r") as reader:
for line in reader.readlines():
parts = line.split()
p2 = float(parts[-1])
if p2 < 0.1:
print line
picked_collected.append(p2)
self.assertIn(p2_less, picked_collected)
def test_rebuild_sequence(self):
pass
#give a sequence
seq_given = "ATGTGTGCCCTTGAAACCCC"
# here we build fake snp file
tmp_file_name = "./fake_snp.rnasnp"
tmp_file_with_line = "./snp_line.rnasnp"
table_head = "SNP w Slen GC interval d pvalue1 ewin interval d_max pvalue2"
describe_line_one = "200 2463 0.5373 1-26 0.0361 0.0943 200 1-53 0.0072 0.4643"
snp_line_picked_out = "200 2463 0.5373 1-26 0.0361 0.0943 200 1-53 0.0072 0.0643"
p2_less = 0.0643
line_num_pick = 9
with open(tmp_file_name, "w") as snp_faker:
snp_faker.write(table_head)
snps = []
for index_nt, nt in enumerate(seq_given):
snps.extend(RNAsnp.mutation_one_site(nt, index_nt+1))
snp_faker.write("\n".join(snps))
with open(tmp_file_with_line, "w") as snps_add_line:
snps_add_line.write(table_head)
snp_lines = []
for snp in snps:
if snps.index(snp) == line_num_pick:
snp_lines.append("\t".join([snp, snp_line_picked_out]))
else:
snp_lines.append("\t".join([snp, describe_line_one]))
snps_add_line.writelines("\n".join(snp_lines))
# use this file as input for pyRNAsnp.get_snp_list.
rebuilded_seq = RNAsnp.rebuild_seq(tmp_file_name)
self.assertEqual(seq_given, rebuilded_seq)
# test how to pick out a line with less p-value
picked_collected = []
with open(tmp_file_with_line, "r") as reader:
for line in reader.readlines():
parts = line.split()
p2 = float(parts[-1])
if p2 < 0.1:
print line
picked_collected.append(p2)
self.assertIn(p2_less, picked_collected)
def test_rnasnp_built_cpd(self):
"""
check the performance after a filter added
:return:
"""
snp_file_name = "./snp_line.rnasnp"
rnasnp_list, rnasnp_list_head = RNAsnp.rnasnp_extractor(snp_file_name)
seq_rebuilt = RNAsnp.rebuild_seq(snp_file_name)
# rnasnp_built_cpd(list_rnasnp, head_list_rnasnp, sequence_string, list_codon=gc.codon_list):
codon_pair = RNAsnp.rnasnp_built_cpd(rnasnp_list, rnasnp_list_head, seq_rebuilt)
for key1 in codon_pair.keys():
if codon_pair[key1]:
print key1, str(codon_pair[key1])
def test_rnasnp_built_cpd(self):
"""
check the performance after a filter added
:return:
"""
snp_file_name = "./snp_line.rnasnp"
rnasnp_list, rnasnp_list_head = RNAsnp.rnasnp_extractor(snp_file_name)
seq_rebuilt = RNAsnp.rebuild_seq(snp_file_name)
# rnasnp_built_cpd(list_rnasnp, head_list_rnasnp, sequence_string, list_codon=gc.codon_list):
codon_pair = RNAsnp.rnasnp_built_cpd(rnasnp_list, rnasnp_list_head,
seq_rebuilt)
for key1 in codon_pair.keys():
if codon_pair[key1]:
print key1, str(codon_pair[key1])
