AttributeError: 'LayoutLine' object has no attribute 'order'

[pk-zhu]

Dear Support,

I hope this message finds you well. I have encountered an issue and would greatly appreciate your assistance.

python -m jcvi.graphics.karyotype seqids.txt layout.txt
[23:40:42] INFO Note: NumExpr detected 56 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. utils.py:148
INFO NumExpr defaulting to 8 threads. utils.py:160
[23:40:43] ERROR Set text.usetex=False. Font styles may be inconsistent. base.py:393
DEBUG Load file layout.txt base.py:37
DEBUG Load file Cdes.bed base.py:37
[23:40:44] DEBUG Load file Peds.bed base.py:37
Traceback (most recent call last):
File "/pub/anaconda3/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/pub/anaconda3/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/pub/anaconda3/lib/python3.8/site-packages/jcvi/graphics/karyotype.py", line 447, in
main()
File "/pub/anaconda3/lib/python3.8/site-packages/jcvi/graphics/karyotype.py", line 427, in main
Karyotype(
File "/pub/anaconda3/lib/python3.8/site-packages/jcvi/graphics/karyotype.py", line 346, in init
layout = Layout(layoutfile, generank=generank)
File "/pub/anaconda3/lib/python3.8/site-packages/jcvi/graphics/karyotype.py", line 78, in init
blocks = self.parse_blocks(fn, i)
File "/pub/anaconda3/lib/python3.8/site-packages/jcvi/graphics/karyotype.py", line 86, in parse_blocks
order = self[i].order
AttributeError: 'LayoutLine' object has no attribute 'order'

head Peds.bed

Ped07D 1762 5299 EVM0015331.1 0 - 1762 5299 255,0,0 5 193,38,68,93,88 0,2591,2665,2928,3449
Ped07D 12578 16711 EVM0022403.1 0 + 12635 16242 255,0,0 10 57,110,58,264,138,52,80,60,81,562 0,700,910,1609,1974,2191,2322,2709,3327,3571
Ped07D 20057 32716 EVM0009251.1 0 - 20057 32716 255,0,0 2 405,210 0,12449
Ped07D 136305 143834 EVM0016564.1 0 + 136429 143311 255,0,0 5 124,116,244,1524,703 0,471,4752,5220,6826
Ped07D 159903 161676 EVM0009065.1 0 + 159903 161676 255,0,0 1 1773 0

Looking forward to your prompt reply.

[Adamtaranto]

Please post your layout.txt file and the head of seqids.txt

[Adamtaranto]

Check that the BED files referred to in your layout file are formatted like this example. They should be tab delimited with 7 cols.

[pk-zhu]

Please post your layout.txt file and the head of seqids.txt

$ cat seqids.txt
A1,A10,A11,A12,A2,A3,A4,A5,A6,A7,A8,A9,B1,B10,B11,B12,B2,B3,B4,B5,B6,B7,B8,B9
Ped01C,Ped01D,Ped02C,Ped02D,Ped03C,Ped03D,Ped04C,Ped04D,Ped05C,Ped05D,Ped06C,Ped06D,Ped07C,Ped07D,Ped08C,Ped08D,Ped09C,Ped09X,Ped10C,Ped10D,Ped11C,Ped11D,Ped12C,Ped12D

$ cat layout.txt

y, xstart, xend, rotation, color, label, va, bed

.6, .1, .9, 0, , Cdes, top, Cdes.bed
.4, .1, .9, 0, , Peds, bottom, Peds.bed

edges

e, 0, 1, Cdes.Peds.anchors.simple

[pk-zhu]

Check that the BED files referred to in your layout file are formatted like this example. They should be tab delimited with 7 cols.

$ cat -A Cdes.bed |head
A1^I141892^I144685^ICde1A1G000010.1^I0^I-^I0$
A1^I191807^I196929^ICde1A1G000020.1^I0^I+^I0$
A1^I199560^I207285^ICde1A1G000030.1^I0^I-^I0$
A1^I223574^I226367^ICde1A1G000040.1^I0^I-^I0$
A1^I237103^I250991^ICde1A1G000050.1^I0^I+^I0$
A1^I452164^I454084^ICde1A1G000060.1^I0^I+^I0$
A1^I886095^I886722^ICde1A1G000070.1^I0^I-^I0$
A1^I958065^I958971^ICde1A1G000080.1^I0^I+^I0$
A1^I1253151^I1264032^ICde1A1G000090.1^I0^I+^I0$
A1^I1565339^I1565842^ICde1A1G000100.1^I0^I-^I0$

$ cat -A Peds.bed |head
Ped08C^I3565^I4156^IEVM0039203.1^I0^I+^I0$
Ped08C^I6470^I10172^IEVM0031106.1^I0^I-^I0$
Ped08C^I24398^I26060^IEVM0033975.1^I0^I-^I0$
Ped08C^I32461^I35845^IEVM0047455.1^I0^I+^I0$
Ped08C^I84099^I88111^IEVM0051843.1^I0^I+^I0$
Ped08C^I113185^I116744^IEVM0024039.1^I0^I-^I0$
Ped08C^I152330^I153353^IEVM0025742.1^I0^I-^I0$
Ped08C^I221686^I224765^IEVM0027074.1^I0^I+^I0$
Ped08C^I227548^I230532^IEVM0030317.1^I0^I+^I0$
Ped08C^I239084^I240491^IEVM0002302.1^I0^I+^I0$

[pk-zhu]

Check that the BED files referred to in your layout file are formatted like this example. They should be tab delimited with 7 cols.

It seems that this BED sample has only six columns. I tried both seven-column and six-column formats, but I still get the same error.

[pk-zhu]

Thank you for your help. This was a careless mistake on my part. I have identified the problem: it was caused by an unintended blank line at the start of the layout.txt file, which occurred when using the echo command.

echo "

y, xstart, xend, rotation, color, label, va, bed

.6, .1, .9, 0, red, C. delicatus, top, Cdes.bed
.4, .1, .9, 0, green, P. edulis, bottom, Peds.bed

edges

e, 0, 1, Cdes.Peds.anchors.simple" > layout.txt