Closed cfz1998 closed 1 year ago
sample1_collinearity.conf
gff1 = sample1.gff
gff2 = sample1.gff
lens1 = sample1.len
lens2 = sample1.len
blast = ../02.mcscanx/sample1.blast
blast_reverse = false
multiple = 1
process = 8
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 25,25
pvalue = 1
repeat_number = 10
positon = order
savefile = sample1.coll
It looks like a problem with pandas. Could you please upload your data so I can test it? Alternatively, you can send it to me separately via email : sunpengchuan@gmail.com
Hi!@SunPengChuan
My data was here. Thank you for your reply!
The GFF file you are processing has issues. Such as Lachesis_group13 Actinidia07289.t1 6088347 6108665 - 489 Lachesis_group13 Actinidia07290.t1 6088770 6091853 - 489
I'll send you the processed GFF file and the script to process it. Actinidia_chinensis.zip
There is something wrong with from collections import defaultdict
in my code. Thanks!
Hi!@SunPengChuan When i use![image](https://user-images.githubusercontent.com/60096719/226176605-5301c01a-8ad6-410c-97b0-286c4287e7d7.png)
wgdi -icl *_collinearity.conf
to find collinearity genes in one genome. I got an error!I don't know why. Thank you for your reply!