SunPengChuan
commented
3 years ago Documentation for installation along with a user tutorial, a default parameter file, and test data are provided. please consult the docs at http://wgdi.readthedocs.io/en/latest/ and https://github.com/SunPengChuan/wgdi-example . here are some videos in https://www.bilibili.com/video/BV1qK4y1U7eK/ and https://www.bilibili.com/video/BV195411P7L1/
Dear Chuan, Thank you very much for your help. I started with example analysis vv1s and followed the instruction but the following tow errors occur in retain and circos steps. 1 /Vitis_vinifera$ wgdi -p total.conf alignment = allignment.csv gff = vv1s.gff lens = vv1s.lens colors = red,blue,gree gap = 50 retention = 0.05 diff = 0.05 remove_delta = (true/false) savefile = index.csv
Polyploidy-index between subgenomes are [] Traceback (most recent call last): File "/home/sajjad/anaconda3/envs/wgd/bin/wgdi", line 10, in
sys.exit(main())
File "/home/sajjad/anaconda3/envs/wgd/lib/python3.9/site-packages/wgdi/run.py", line 208, in main
module_to_run(arg)
File "/home/sajjad/anaconda3/envs/wgd/lib/python3.9/site-packages/wgdi/run.py", line 174, in module_to_run
return switcher.get(argument)()
File "/home/sajjad/anaconda3/envs/wgd/lib/python3.9/site-packages/wgdi/run.py", line 131, in run_pindex
p.run()
File "/home/sajjad/anaconda3/envs/wgd/lib/python3.9/site-packages/wgdi/pindex.py", line 66, in run
p = self.cal_pindex(alignment)
File "/home/sajjad/anaconda3/envs/wgd/lib/python3.9/site-packages/wgdi/pindex.py", line 98, in cal_pindex
return sum(data)/len(data)
ZeroDivisionError: division by zero
Please help me to resolve this issue.
2
TH 2nd query is regarding the final circos map, from where i can get the following files !) ancestor location 2) ancestor 3) It also shows that column names attribute is missing.