jakobnissen / alen

Simple terminal alignment viewer

Welcome to my GitHub page

I'm Jakob, a biologist-turned-programmer, happy in my role as a research software engineer.

I work as an assistant professor at CPR, Copenhagen University researching metagenomics with particular interest in virus- and plasmid metagenomics. Biologically, my interests are in phylogenetics, molecular evolution and sub-genomic replicons. On the computer science side, I'm a Julia, Rust and Python enthusiast, contributing to BioJulia and Julia. I particularly enjoy writing optimized and generic software packages for bioinformatics.

Highlighted work:

Selected repositories

• Vamb - variational autoencoders for metagenomic binning
• Course material for introductory Python course
• Alen - simple terminal alignment viewer.
• BinBencherBackend.jl - metagenomic binning benchmarking and analysis software
• LibDeflate.jl - bindings to the fast de/compression library libdeflate
• StackCollections.jl - optimized, fixed-bit collections in Julia
• MinHash.jl - efficient, generic minhashing.

Repositories I maintain

• BioSymbols.jl
• BioSequences.jl
• FASTX.jl
• Automa.jl
• WIP: MemoryViews.jl
• WIP: XAMAuxData.jl
• WIP: PairwiseMappingFormat.jl

alen's Issues

Installation info for newbies

Hi Jakob,

I am missing information on how to install alen. I have downloaded to compressed file to my download folder (I am running Windows subsystem for Linux) and uncompressed it. So, where do I put the files then?

Best,
Rikki

modified RNA residues not working correctly

Hi,
i wanted to say thank you for making this alignment viewer, i really like it!

I have had some problems viewing MSAs of RNAs with modified residues.
The problem seems to be that with all the modified RNA residues that exist, the sequences contain a lot of unusual characters.

A database of modified RNA residues can be found here:
https://iimcb.genesilico.pl/modomics/modifications

There seem to be two problems as far as i can see

• unicode characters, e.g. °

>tdbR00000266|Bos_taurus|9913|Leu|°AA
-GUCAGLAUGLCMGAGU--GGDCPAAGGCLCCAGACU°AAKPPCUGGJ-CPCC---GUAU----GGAGG-?GUGGGTPCG"AUCCCACUUCUGACACCA

Error message:

ERROR when loading FASTA: Not all input sequences are the same length. Expected sequence length 99, seq "tdbR00000266|Bos_taurus|9913|Leu|°AA" has length 100.

• autodetection trying to interpret sequences as amino-acids

>tdbR00000270|Avian_myeloblastosis_virus|11866|Met|BAU
-GCCUCCUUALCGCAGDA-GGN--AGCGCRPCAGPCUBAU6APCUGAAG-------------------7D??UGAGTPCG"ACCUCAGAGGGGGCACCA

Error message:

ERROR when loading FASTA: Sequence "tdbR00000270|Avian_myeloblastosis_virus|11866|Met|BAU" cannot be understood as amino acids.

My suggestion would be to have additional command-line options to

• allow unicode
• force dna, rna, aa mode without autodetect

Not sure how to deal with it in visualisation. I guess one color for any nonstandard RNA base would be ok.

What do you think? I could try and make the changes if you agree

Data source:

Data was downloaded from tRNAdb:

http://trna.bioinf.uni-leipzig.de/DataOutput/Search

On the Search Database page, choose tRNA sequences and then press the search database button. This will return RNA sequences with modified sequences. You can save them by selecting the select all sequences of search checkbox on the search results page, and then saving the sequences by choosing Download alignment in the drop down button next to the checkbox.

`tmux`-friendly controls?

Hi Jakob! This thing looks cool, thanks!

I recognize that it might not be a common usecase for alen, but I would routinely use it to browse alignments in an ssh session through tmux on macOS. Taken together, it superseeds most of the control key sequences that seem to be hardcoded in alen 😞 specifically, Ctrl-Shift-arrows do not work and ctrl-J jumps to the next pane...

It would be helpful to me if the key bindings were remappable! Otherwise, an alternative control scheme involving less ctrls and shifts would also work.

Cheers,
Nikita

Work with stdin

It would be nice to work with stdin, but unfortunately, crossterm does not seem to support it at the moment.

As soon as crossterm fixes the issue or provide a workaround, implement reading from stdin.

Alignment::calculate_order should operate on original_index of entries

Currently it operates on the current index of entries, not the original index.
This causes mis-sorting if the input sequences were already permuted before the order is calculated.

Implement CI with GitHub Actions

Steps

• PR job which runs a build, rustfmt, and clippy
• Master build job with status badge in README.md
• New release job, which builds a Changelog from commit history and opens a draft release
• New release job attaches pre-built binaries for Linux
• New release job attaches pre-built binaries for MacOS (x86_64)

---

I'm a big believer that every open source project destined for success must make contributions (and maintenance) easy. A solid CI is a cornerstone of that.

If you can spare a week or two, I'd offer to do this for you.