def test_bad_args():
# make sure bad arguments raise errors
with pytest.raises(TypeError):
relative_adaptiveness()
with pytest.raises(TypeError):
relative_adaptiveness(sequences=["AAC"], RSCUs=RSCU(["AAC"]))
from Bio import SeqIO
from Bio.Seq import Seq
from CAI import RSCU
from matplotlib import pyplot as plt
import numpy as np
for seq_record in SeqIO.parse("KRas.gb", "genbank"):
for f in seq_record.features:
rscu_list = []
if f.type == 'CDS':
feature_seq = f.location.extract(seq_record).seq
coding_result = Seq(str(feature_seq))
# 新建一个列表,列表才能作为输入数据
rscu_list.append(coding_result)
#print(rscu_list)
codon_pre = RSCU(rscu_list)
#print(codon_pre)
# 满足rscu不为空就退出
if len(rscu_list):
break
code = []
value = []
for k in codon_pre:
code.append(k)
values = codon_pre[k]
value.append(values)
plt.switch_backend('Agg')
plt.figure(figsize=(20, 6), dpi=80)
width = 0.8
def test_arg_equivalence():
# should be able to take either reference sequences or an RSCU dict
assert relative_adaptiveness(sequences=["AAC"]) == relative_adaptiveness(
RSCUs=RSCU(["AAC"]))