Is Perl a write only language?

I am sick and tired of hearing this, so let's put it this to the test. Assume you know little of Perl, or any programming language for that matter. Can you parse the code?

https://chrisarg.github.io/Killing-It-with-PERL/2023/12/06/Is-Perl-a-write-only-language.html

I hope the piece above is the first in a series to convince people to consider the reality before passing judgement. It was inspired by one of our research analysts discovering Perl and awk to simplify their l…

Hash of Arrays Deathmatch : Native Perl vs. DBM::Deep vs. Redis

Sometimes one has to make compromises between speed of execution and memory, other times one may not have to be. While working towards a fairly (at least in my mind) complete solution to map Nanopore Sequencing files, I ran against the need to create and access fairly large hash of arrays (think of 1M - 100Mof keys), with each array itself consisting of a a fixed number of elements.
The hash of arrays is a fairly straightforward and fast data structure to create in Perl, the memory overhead can be substantial as the number of keys and values scale upwards.…

Of Go, C, Perl and fastq file conversion Vol IV : gone in 60 seconds (or less)

In the final part of this series, we will test the performance of the four parsers, in a scenario emulating the batch analysis of sequencing data. We will use the sample fastq file 3_OHara_S2_rbcLa_2019_minq7.fastq from https://zenodo.org/record/3736457. This is a 35MB file of 21791 long sequences for a nanopore experiment. Download the data and save them to a directory in your hard disk. Then use the following bash time_fastq2a_shell.txt (change the extension to .sh before running!) to process this file 500…

Of Go, C, Perl and fastq file conversion Vol III : pledging allegiance to the flag

In the previous entry, we presented a regex based fastq parser. As the regex engine maps to a finite state automaton, we should be able to rewrite the parser without regular expressions, using flags to keep track of the part of the record we are at. The code is straightforward, but lacks the elegance of the regex parser. It is provided as a possibly faster alternative to the regular expression implementation.

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Of Go, C, Perl and fastq file conversion Vol II : the Jedi regex

In the second part of this series about fast parsers for sequencing applications,  I will review the code for the regex based parser. This is shown below (I use v5.38, as you should! because the year is 2023 and you should not have to type use strict; use warnings)

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