Closed Alalakikun closed 1 year ago
You need to check that: the first column of the GFF file and the LENS file are consistent. The two columns of IDs in the BLAST file should be consistent with the second column of GFF1 and GFF2.
I'm not sure what's wrong with my content, and I have confirmed it many times
They look good. Could you upload your files for me to test? You can send them to my email: sunpengchuan@gmail.com.
Yes, I have sent it to you
I have not received it yet.
and now?
[dotplot] blast = Cg.blastp gff1 = Cg_out.gff gff2 = Cg_out.gff lens1 = Cg.len lens2 = Cg.len genome1_name = Genome1 name genome2_name = Genome2 name multiple = 1 score = 100 evalue = 1e-5 repeat_number = 10 position = end blast_reverse = false markersize = 0.5 figsize = 10,10 savefig = cg.png
I tested it in Python 3.11 and it produced results without any errors.
I am using wgdi from the conda package and the python version is 3.11. I will try again with python alone,thank you very much for your help
Hey @SunPengChuan could you specify what is the third coulm of lens input file? I couldnt find anywhere. maybe I missed in documents.
You can refer to the test files from a previous project available at this https://github.com/SunPengChuan/wgdi-example. Additionally, detailed instructions on the format of the lens files can be found in the https://wgdi.readthedocs.io/en/latest/usage.html. Moreover, I have provided a method on this https://github.com/SunPengChuan/wgdi-example/tree/main/code, which is not universal and may require some adjustments.
We prepared three input files according to the example, but an error occurred after the last step "wgdi -d total.cof" was enteredTraceback (most recent call last): File "/home/bycl0009/miniconda3/envs/wgdi/bin/wgdi", line 10, in
sys.exit(main())
^^^^^^
File "/home/bycl0009/miniconda3/envs/wgdi/lib/python3.11/site-packages/wgdi/run.py", line 163, in main
module_to_run(arg, value)
File "/home/bycl0009/miniconda3/envs/wgdi/lib/python3.11/site-packages/wgdi/run.py", line 122, in module_to_run
run_subprogram(program, conf, name)
File "/home/bycl0009/miniconda3/envs/wgdi/lib/python3.11/site-packages/wgdi/run.py", line 87, in run_subprogram
r.run()
File "/home/bycl0009/miniconda3/envs/wgdi/lib/python3.11/site-packages/wgdi/dotplot.py", line 98, in run
gff1 = base.gene_location(gff1, lens1, step1, self.position)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/bycl0009/miniconda3/envs/wgdi/lib/python3.11/site-packages/wgdi/base.py", line 214, in gene_location
gff.loc[group.index, 'loc'] = (dict_chr[name]+group[position])*step