LayoutLine' object has no attribute 'color'

[Zefeng-Wu]

#y,xstart,xend,rotation,color,label,va,bed
.6,.1,.8,0,m,Grape,top,rice.bed
.4,.1,.8,0,k,Peach,top,ara.bed
#edges
e,0,1,rice.ara.anchors.simple

[wyim-pgl]

Check the rice.ara.anchors.simple file

[Zefeng-Wu]

Thanks,but this file seems right.

OS01G0901000 OS01G0908700 AT1G67530 AT1G67800 38 +
OS01G0847600 OS01G0856500 AT2G37790 AT2G38120 44 +
OS01G0844200 OS01G0854000 AT2G39705 AT2G39980 49 +
OS01G0836600 OS01G0842200 AT2G37360 AT2G37650 38 +
OS01G0818100 OS01G0832900 AT2G40120 AT2G40815 88 -
OS01G0846800 OS01G0851400 AT3G53830 AT3G54130 33 +

[wyim-pgl]

seqids and head of rice.bed ?

[Zefeng-Wu]

seqids:
1,2,3,4,5,6,7,8,9,10,11,12
1,2,3,4,5

rice.bed:
1 2983 10815 OS01G0100100 0 +
1 11218 12435 OS01G0100200 0 +
1 11372 12284 OS01G0100300 0 -
1 12721 15685 OS01G0100400 0 +
1 12808 13978 OS01G0100466 0 -
1 16399 20144 OS01G0100500 0 +
1 22841 26892 OS01G0100600 0 +

[wyim-pgl]

Ref #20

Please remove the bottom blank line in "layout" file.

[Zefeng-Wu]

I have tried, but it gave these error
File "/usr/lib/python2.7/runpy.py", line 162, 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-0.7.3-py2.7.egg/jcvi/graphics/karyotype.py", line 320, in
main()
File "/usr/local/lib/python2.7/dist-packages/jcvi-0.7.3-py2.7.egg/jcvi/graphics/karyotype.py", line 308, in main
Karyotype(fig, root, seqidsfile, layoutfile)
File "/usr/local/lib/python2.7/dist-packages/jcvi-0.7.3-py2.7.egg/jcvi/graphics/karyotype.py", line 265, in init
t = layout[i]
IndexError: list index out of range

[Zefeng-Wu]

Thank you very much , i have success

[wyim-pgl]

IndexError: list index out of range

= Bottom blank line in "Seqids" file

[Zefeng-Wu]

Yeah, i have noticed it, tks