一：数据准备

还是用到上一步生成的ath.aly.anchors和ath.aly.anchors.new文件

1. 创建如下三个文件

• seqids: 需要展现哪些序列
• layout: 不同物种的在图上的位置
• .simple: 从.anchors文件创建的更简化格式
  第一步，创建.simple文件

python -m jcvi.compara.catalog ortholog --no_strip_names ath aly
python -m jcvi.compara.synteny screen --minspan=30 --simple ath.aly.anchors ath.aly.anchors.new

第二步, 创建seqids文件，非常简单，就是需要展示的scaffold或染色体的编号

scaffold_1,scaffold_2,scaffold_3,scaffold_4,scaffold_5,scaffold_6,scaffold_7,scaffold_8
Chr1,Chr2,Chr3,Chr4,Chr5

第三步，创建layout文件，用于设置绘制的一些选项。

# y, xstart, xend, rotation, color, label, va,  bed
 .6,     .2,    .8,       0,      , Alyrata, top, aly.bed
 .4,     .2,    .8,       0,      , Athaliana, top, ath.bed
# edges
e, 0, 1, aly.ath.anchors.simple

注意, #edges下的每一行开头都不能有空格

最后运行下面的命令，会得到一个karyotype.pdf

python -m jcvi.graphics.karyotype seqids layout

单身在这里报错了，还没找到是什么原因，有没有大佬知道，告诉我一下怎么解决！下面是报错的日志：

$python -m jcvi.graphics.karyotype seqids layout
21:53:50 [base] Load file `layout`
21:53:50 [base] Load file `aly.bed`
21:53:51 [base] Load file `ath.bed`
Traceback (most recent call last):
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 422, in <module>
    main()
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 409, in main
    generank=(not opts.basepair),
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 358, in __init__
    tr = Track(root, lo, gap=gap, height=height, lw=lw, draw=False)
  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/graphics/karyotype.py", line 146, in __init__
    ratio = span / total
ZeroDivisionError: float division by zero