search

tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
712 stars 185 forks source link

AttributeError: 'LayoutLine' object has no attribute 'color #616

Open mixle18 opened 6 months ago

mixle18 commented 6 months ago

Hi, I am trying to run microsynteny And i am getting this issue with colour. Can you help?

(allmap) safflower2@safflower2:/media/safflower2/Data/megha/validation/synteny/data/pairwise$ python -m jcvi.graphics.karyotype seqids layout [04:22:37] DEBUG Load file layout base.py:34 DEBUG Load file saf_chinese.bed base.py:34 [04:22:38] DEBUG Load file saf_du.bed base.py:34 Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/karyotype.py", line 469, in main() File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/karyotype.py", line 447, in main Karyotype( File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/karyotype.py", line 350, in init layout = Layout(layoutfile, generank=generank, seed=seed) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/karyotype.py", line 87, in init self.assign_colors(seed=seed) File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/base.py", line 151, in assign_colors self.assign_array("color", colorset) File "/home/safflower2/anaconda3/envs/allmap/lib/python3.11/site-packages/jcvi/graphics/base.py", line 141, in assign_array if not getattr(x, attrib): ^^^^^^^^^^^^^^^^^^ AttributeError: 'LayoutLine' object has no attribute 'color