Pedro Queirós

Adding another protein function annotation tool

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Hello, We have recently published a protein function annotation tool (i.e., [Mantis](https://github.com/PedroMTQ/mantis)) and are now interested in building metabolic networks using the annotations provided from this tool as a seed...

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.

http://www.essentialgene.org/

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)

Selected labels highlight

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Feature description --------- For document labelling would it be possible to make the highlighted labels pop out slightly? This is not a big issue for a small set of labels,...

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...

Thanks for the very nice library. I really like how obvious and easy is is to use. I was wondering if there are any plans to add a per-domain auto-throttle...