From 37096948fce9090ea2918e14991d860e204c2480 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 2 Aug 2023 17:22:10 +0200
Subject: [PATCH] First list of libraries.

---
 README.md | 219 ++++++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 162 insertions(+), 57 deletions(-)

diff --git a/README.md b/README.md
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 # Some useful Python libraries
 
+The current plan is to use this repository to list (and possibly demonstrate the use of) some Python libraries I use, have used or may want to use on day.
 
+## TODO
 
-## Getting started
+* Complete the list
+* Add citations
+* Add Jupyter notebooks to demonstrate usage
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+## General
 
-## Add your files
+### cytoolz
 
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+Lots of useful functions for functionnal programming fun, hopefully faster than pytoolz.
 
+The documentation is that of pytoolz: <https://toolz.readthedocs.io/en/latest/>
+
+URL: <https://pypi.org/project/cytoolz/>
+
+### dask
+
+I once tried a few stuff from this library to run things in parallel.
+
+URL: <https://www.dask.org/>
+
+### snakemake
+
+To build workflows, with versatility provided by Python.
+
+My advice: don't use `expand`, but standard Python constructs instead.
+
+Using input functions, it is possible to assemble quite complex workflows.
+
+URL: <https://snakemake.readthedocs.io/en/stable/>
+
+### nimpy
+
+To build Python modules using Nim.
+I haven't used it yet.
+
+URL: <https://github.com/yglukhov/nimpy>
+
+## Data analysis
+
+### scipy
+
+I sometimes use the `stats` module, and otherwise in combination with other libraries that depend on scipy.
+
+URL: <https://docs.scipy.org/doc/scipy/index.html>
+
+### numpy
+
+Like with scipy, I usually use it in combination with
+
+URL: <https://numpy.org/>
+
+### pandas
+
+Provides lots of ways to handle tabular data.
+
+URL: <https://pandas.pydata.org/>
+
+### scikit-learn
+
+URL: <https://scikit-learn.org/stable/>
+
+### matplotlib
+
+URL: <https://matplotlib.org/>
+
+### seaborn
+
+Built on top of matplotlib, to provide some common graphical representations.
+
+URL: <https://seaborn.pydata.org/>
+
+### plotnine
+
+One of the Python "versions" of ggplot.
+
+URL: <https://plotnine.readthedocs.io/en/stable/index.html>
+
+### plydata
+
+"dplyr" for pandas.
+
+<https://plydata.readthedocs.io/en/stable/index.html>
+
+### networkx
+
+Useful for some optimisation problems that can be modelled using graphs.
+
+URL: <https://networkx.org/>
+
+### polars
+
+Promises efficient data frames to use instead of pandas.
+I haven't tried it yet as of august 2023.
+
+URL: <https://www.pola.rs/>
+
+### rpy2
+
+I have used it to run functions provided by R packages from Python because programming with R was frustrating.
+However, using rpy2 was not really a pleasant programming experience either.
+
+URL: <https://rpy2.github.io/>
+
+## Bioinfofmatics
+
+### biopython
+
+I actually rarely use it, but this is a reference in terms of handling biology-related data.
+
+URL: <https://biopython.org/>
+
+### pysam
+
+I use it to parse bam of vcf files.
+
+URL: <https://pysam.readthedocs.io/en/latest/api.html>
+
+### cyvcf2
+
+I plan to try it to parse vcf files.
+
+URL: <https://brentp.github.io/cyvcf2/index.html>
+
+### mappy
+
+I use its fast fata / fastq parser:
+
+```{python}
+from mappy import fastx_read
+
+for (name, seq, qual) in fastx_read("path_to_data.fastq"):
+    pass
 ```
-cd existing_repo
-git remote add origin https://gitlab.pasteur.fr/bli/some-useful-python-libraries.git
-git branch -M main
-git push -uf origin main
-```
 
-## Integrate with your tools
+URL: <https://pypi.org/project/mappy/>
+
+### gffutils
+
+To work with genome annotations.
+
+URL: <https://daler.github.io/gffutils/>
 
-- [ ] [Set up project integrations](https://gitlab.pasteur.fr/bli/some-useful-python-libraries/-/settings/integrations)
+### pybedtools
 
-## Collaborate with your team
+Wrapper around bedtools, to work with genomic intervals.
 
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+URL: <https://daler.github.io/pybedtools/>
 
-## Test and Deploy
+### biotite
 
-Use the built-in continuous integration in GitLab.
+I used some of the tools it provides to display sequences, with colours:
+<https://www.biotite-python.org/apidoc/biotite.sequence.graphics.html#module-biotite.sequence.graphics>
 
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+URL: <https://www.biotite-python.org/>
 
-***
+### parasail
 
-# Editing this README
+To perform pairwise sequence alignemnt.
 
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
+URL: <https://github.com/jeffdaily/parasail-python>
 
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+### ete
 
-## Name
-Choose a self-explaining name for your project.
+To display phylogenetic trees.
 
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+URL: <http://etetoolkit.org/>
 
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+### dendropy
 
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+To manipulate phylogenetic trees.
 
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
+URL: <https://dendropy.org/>
 
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+### p4
 
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+Versatile MCMC phylogeny building using Python.
 
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
+URL: <https://p4.nhm.ac.uk/>
 
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
+### scikit-bio
 
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+I have used it to handle distance matrices: <http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.html>
 
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+URL: <http://scikit-bio.org/>
 
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
+### scikit-allel
 
-## License
-For open source projects, say how it is licensed.
+For population genetics.
 
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+URL: <https://scikit-allel.readthedocs.io/en/stable/index.html>
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