bed文件中染色体名称跟seqid中的染色体名称不一致,你检查一下
您好!我在进行python版mcscan得运行,但是运行到python -m jcvi.graphics.karyotype seqids layout 时,提示错误。
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/usr/local/lib/python2.7/dist-packages/jcvi/graphics/karyotype.py", line 330, in <module>
main()
File "/usr/local/lib/python2.7/dist-packages/jcvi/graphics/karyotype.py", line 318, in main
Karyotype(fig, root, seqidsfile, layoutfile)
File "/usr/local/lib/python2.7/dist-packages/jcvi/graphics/karyotype.py", line 294, in __init__
tr = Track(root, lo, gap=gap, height=height, lw=lw, draw=False)
File "/usr/local/lib/python2.7/dist-packages/jcvi/graphics/karyotype.py", line 139, in __init__
ratio = span / total
ZeroDivisionError: float division by zero
我得几个文件是
layout
# y, xstart, xend, rotation, color, label, va, bed
.6, .1, .8, 0, , ZM, top, ZM.bed
.4, .1, .8, 0, , SB, top, SB.bed
# edges
e, 0, 1, ZM.SB.anchors.simple
bed文件:
seqid
chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10
chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10
不知道如何处理这个问题,请您指教。谢谢!
还可以排查一下染色体名称:
可以看看这个:https://www.omicsclass.com/question/1605 还有这个:https://www.omicsclass.com/article/572
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