Unix-Pledge VS bioawk

Compare Unix-Pledge vs bioawk and see what are their differences.

Unix-Pledge

Perl support for pledge(2) syscall (by rfarr)

bioawk

BWK awk modified for biological data (by lh3)
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Unix-Pledge bioawk
1 7
7 572
- -
0.0 0.0
almost 5 years ago over 1 year ago
Perl C
- -
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.

Unix-Pledge

Posts with mentions or reviews of Unix-Pledge. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-09-07.

bioawk

Posts with mentions or reviews of bioawk. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-05-11.
  • Any links to R-scripts for common NGS pipelines?
    2 projects | /r/bioinformatics | 11 May 2023
    Data wrangling is actually what awk excels at, and it's generally much more concise than R for that sort of thing. I'm aware that a lot of awk one liners look like gibberish to the uninitiated, but it actually makes a lot of sense when you understand the pattern-action structure of awk programs. It is also installed on any *nix system, there's no need to worry about installing dependencies or setting up virtual environments. And it's several times faster than R. Also Bioawk is glorious.
  • Is BioAwk frequently used, or even useful?
    2 projects | /r/bioinformatics | 5 May 2023
    A few months ago, I learned about this utility known as bioawk, written by Heng Li of samtools fame. Apparently, it is essentially a tweaked version of awk, with some extra goodies added for parsing and processing of bioinformatics file formats. While the functionality seems cool, I was wondering whether it is worth installing on my server, and incorporating into our workflows, because it seems so niche. I have not seen many references to it. Or is it better if we stick to Python scripts for this sort of work? Are there any computational speed advantages, etc. that bioawk offers over regular Python scripts for processing of, let's say, BED files or VCF files?
  • What are the most useful cutting edge tools I should learn for bioinformatics?
    3 projects | /r/bioinformatics | 26 Apr 2023
  • My boss is considering letting me take a programming course if I have some good reasons why.
    2 projects | /r/labrats | 13 Apr 2023
    Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.
  • What are strictly data analysis jobs?
    3 projects | /r/labrats | 22 Feb 2023
    On the other hand, some of the techniques to set the ground for data analysis are equally valuable in other situations. The two installments about regular expressions on programming historian Understanding Regular Expressions and Cleaning OCR’d text with Regular Expressions, for example. They have no relevance to handling chemicals in the lab, yet since then, I find myself working with data files more efficiently, than earlier because of grep, an utility in Linux to crawl across data files. Or AWK, actually picking up theses "regexes", which I find generally useful since Benjamin Porter's "Hack the planet's text" (presentation video, and exercise video) with its link back to chem/bio e.g., to bioawk (btw, there equally is biopython, too).
  • Help they’re turning me into a programmer
    3 projects | /r/labrats | 13 Feb 2023
    Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...
  • Awk: The Power and Promise of a 40-Year-Old Language
    4 projects | news.ycombinator.com | 7 Sep 2021
    There's even a version of awk specifically designed for bioinformatics that natively knows how to handle fasta, fastq, and bam files, among other formats.

    https://github.com/lh3/bioawk

What are some alternatives?

When comparing Unix-Pledge and bioawk you can also consider the following projects:

cligen - Nim library to infer/generate command-line-interfaces / option / argument parsing; Docs at

csvquote - Enables common unix utlities like cut, awk, wc, head to work correctly with csv data containing delimiters and newlines

orange - 🍊 :bar_chart: :bulb: Orange: Interactive data analysis

zarp - The Zavolab Automated RNA-seq Pipeline

MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.

Biopython - Official git repository for Biopython (originally converted from CVS)

readfq - Fast multi-line FASTA/Q reader in several programming languages

tiny_python_projects - Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.

dsutils - Command-line tools for doing data science

vcftools - A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

OpenRefine - OpenRefine is a free, open source power tool for working with messy data and improving it