程序中的文件是genbank文件,只要是染色体就可以,想达到染色体上有注释的效果
代码中features为空了,不知道哪里出错了
from reportlab.lib.units import cm
from Bio.Graphics import BasicChromosome
entries = [("Chr I", "1.0.gb"),
("Chr II", "2.gb"),
("Chr III", "3.gb"),
("Chr IV", "4.gb"),
("Chr V", "5.gb")]
for (name, filename) in entries:
record = SeqIO.read(filename, 'genbank')
print(name, len(record))
max_len = 30427671 #最大长度
telomere_length = 10000000 #假设
chr_diagram = BasicChromosome.Organism()
chr_diagram.page_size = (29.7*cm, 21*cm) #A4 大小
for index, (name, filename) in enumerate(entries): # 从entries中循环
record = SeqIO.read(filename,"genbank")
length = len(record)
print(length)
features = [f for f in record.features if f.type=="tRNA"]
print(record.features)
print(features)
#Record an Artemis style integer color in the feature's qualifiers,
#在特性的限定符中记录Artemis风格的整数颜色
#1 = Black, 2 = Red, 3 = Green, 4 = blue, 5 =cyan, 6 = purple
for f in features:
f.qualifiers["color"] = [index + 2]
Chr1 30427671
Chr 2 19698289
Chr 3 23459830
Chr 4 18585056
Chr 5 26975502
30427671
19698289
[SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(19698289), strand=1), type='source')]
23459830
[SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(23459830), strand=1), type='source')]
18585056
[SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(18585056), strand=1), type='source')]
26975502
[SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(26975502), strand=1), type='source')]
[]
for index, (name, filename) in enumerate(entries): # 从entries中循环
record = SeqIO.read(filename,"genbank")
length = len(record)
print(length)
features = [f for f in record.features if f.type=="tRNA"]
print(record.features)
print(features)
不知道这几行错哪里了,导致features为空,或者是文件不对
feature应该不为空
相关链接在这,是关于染色体17.2节下半段
https://biopython-cn.readthedocs.io/zh_CN/latest/cn/chr17.html#id12