Question

我正在尝试使用biopython（http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec345）重新创建带注释的染色体。我有一个测试代码，可以创建一个染色体和一个带注释的功能（5,10，＆＃34; 1＆＃34;，＆＃34; Gm18_5133882_G_A＆＃34;，＆＃34;蓝＆＃34;）。

from reportlab.lib.units import cm
from Bio.Graphics import BasicChromosome
max_len = 150000 #Could compute this
telomere_length = 50000 #For illustration

chr_diagram = BasicChromosome.Organism()
chr_diagram.page_size = (29.7*cm, 21*cm) #A4 landscape
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the scale to the MAXIMUM length plus the two telomeres in bp,
#want the same scale used on all five chromosomes so they can be
#compared to each other
cur_chromosome.scale_num = max_len + 2 * telomere_length

#Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = telomere_length
cur_chromosome.add(start)

#location of the chromosome
features = 5, 10, "1", "Gm18_5133882_G_A", "blue"

#Add a body - again using bp as the scale length here.
body = BasicChromosome.AnnotatedChromosomeSegment(max_len, features)
body.scale = max_len
cur_chromosome.add(body)

#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = telomere_length
cur_chromosome.add(end)

#This chromosome is done
chr_diagram.add(cur_chromosome)

chr_diagram.draw("simple_chrom.pdf", "Dummy_chromsome")

它给出了以下错误，并且根据biopython脚本注释功能应该作为SeqFeature对象或元组提供（＆＃34;要素可以是SeqFeature对象，也可以是值的元组：start（int），end（int），strand（+ 1，-1，O或None），label（字符串），ReportLab颜色（字符串或对象）和可选的ReportLab填充颜色。＆＃34;）。我不确定问题在哪里，任何帮助将不胜感激。

TypeError                                 Traceback (most recent call last)
<ipython-input-67-a67e6230693f> in <module>()
 25 chr_diagram.add(cur_chromosome)
 26 
 ---> 27 chr_diagram.draw("simple_chrom.pdf", "Dummy_chromsome")

User/lib/python2.7/site-packages/Bio/Graphics/BasicChromosome.pyc in draw(self,     output_file, title)
146 
147             # do the drawing
--> 148             sub_component.draw(cur_drawing)
149 
150             # update the locations for the next chromosome

User/lib/python2.7/site-packages/Bio/Graphics/BasicChromosome.pyc in draw(self, cur_drawing)
274             sub_component._left_labels = []
275             sub_component._right_labels = []
--> 276             sub_component.draw(cur_drawing)
277             left_labels += sub_component._left_labels
278             right_labels += sub_component._right_labels

User/lib/python2.7/site-packages/Bio/Graphics/BasicChromosome.pyc in draw(self, cur_drawing)
419         self._draw_subcomponents(cur_drawing)  # Anything behind
420         self._draw_segment(cur_drawing)
--> 421         self._overdraw_subcomponents(cur_drawing)  # Anything on top
422         self._draw_label(cur_drawing)
423 

User/lib/python2.7/site-packages/Bio/Graphics/BasicChromosome.pyc in _overdraw_subcomponents(self, cur_drawing)
667             except AttributeError:
668                 #Assume tuple of ints, string, and color
--> 669                 start, end, strand, name, color = f[:5]
670                 color = _color_trans.translate(color)
671                 if len(f) > 5:

TypeError: 'int' object has no attribute '__getitem__'

Answer 1

更改

features = 5, 10, "1", "Gm18_5133882_G_A", "blue"

到

features = [(5, 10, +1, "Gm18_5133882_G_A", "blue")]

应该让它发挥作用。

请注意：

BasicChromosome.AnnotatedChromosomeSegment()会获取一系列功能，因此即使您只有一个功能"Gm18_5133882_G_A"，也必须在列表中。
Strand应该是+1，-1或None。因此，如果您将"1"作为链，Biopython会将其解释为None。

使用biopython制作带注释的染色体

1 个答案: