mantis
mantis copied to clipboard
PedroMTQ
A package to annotate protein sequences
Hello developer, First of all thank you very much for this great pipeline. Now, I ran Mantis on a gene prediction made by Braker. But the gff output is wrong....
Hi, I installed mantis using conda install which went fine: conda create -p /tools/Miniconda3/envs/mantis_annotate -c conda-forge -c bioconda mantis_pfa However, when I run: mantis setup I get the following error:...
On two very different systems I'm getting stuck at the same place in the setup. ``` mantis setup ... Merging profiles in /lizardfs/erikg/miniconda3/lib/python3.8/site-packages/References/NCBI/986/to_merge/ Concatenating files into /lizardfs/erikg/miniconda3/lib/python3.8/site-packages/References/NCBI/986/986_merged.hmm ``` The setup...
Mantis seems to spawn more processes than available cores and to run out of memory during the setup step. I ran it with 5 cores and 20 Gb, and during...
Add putative operon prediction by coordinate and functional clustering
As pointed out by @hbckleikamp Diamond needs to be setup differently in order to annotate peptides. See https://github.com/bbuchfink/diamond/discussions/469 for details from author.
E.g., if using a tigrfam custom DB then if the custom db has `tigrfam` in its name then issues will arise: elif 'tigrfam' in hmm_file: self.get_link_tigrfam(dict_hmms) self.is_essential(dict_hmms)
 I just fetched the package from bioconda the mantis_pfa=1.5.5, but when I try to run it, this error above pops out that it never happened before. I don't know...
The purpose of this PR is to overhaul the codebase via multiple steps: - improve architecture and class inheritance (e.g., better procedure separation) - re-organizing codebase for clearer role separation...