Refactor for ver 1.1.0 - Githubissues

zavolanlab / bindz-rbp

RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.

https://github.com/zavolanlab/bindz-rbp

Apache License 2.0

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Refactor for ver 1.1.0 #55

Closed AngryMaciek closed 2 years ago

AngryMaciek commented 3 years ago

Refactor the whole repository before the next release.

[x] rename to bindz-rbp
[x] update rulegraph image
[x] CONTRIBUTING
[x] ~check CodeFactor sheild~ I am not an admin of this organisation therefore I cannot hook up CodeFactor
[x] what about local/cluster and conda/singularity nomenclature?
[x] add singularity local test in the CI
[x] ~clean ATTRACT parsing~
[x] test cluster integration tests execution (2x)
[x] PDF with heatmap visualisation: long sequqnces / lots of PWMs <?>
[x] documentation.md
[x] README

AngryMaciek commented 2 years ago

what about local/cluster and conda/singularity nomenclature?

These names appear only under tests directory, it is therefore fine, everything that is under that directory is designed for developers, not end users. and developers know how to read these files.

CI tests both conda and singularity execution for local

cluster execution is tailored to sciCORE cluster and needs to be tested manually on our filesystem by the developers.

AngryMaciek commented 2 years ago

clean ATTRACT parsing

There is nothing to clean, the pipeline is designed to use a custom set of MotEvo-formatted PWMs, provided by the user. Manual curation of a PWM set is outside the scope of this tool; ATtRACT db download/reformat is just an additional functionality. However, it is up to the user/server to set up a directory of "clean" PWMs.

AngryMaciek commented 2 years ago

PDF with heatmap visualisation: long sequqnces / lots of PWMs <?>

Static plots work fine up to certain constraints: max sequence length: 150, max n.o. PWMs scanned: ~200.

For the pipeline itself it is fine, in the web server we will have the heatmaps dynamically generated in a website, presenting RBP sites together with the miRNA binding sites (Flask?).