- About: I like to use Perl for material other than text.
Posted Is Perl a write only language? to chrisarg
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?
I hope the piece…
Posted Hash of Arrays Deathmatch : Native Perl vs. DBM::Deep vs. Redis to chrisarg
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…
Commented on Of Go, C, Perl and fastq file conversion Vol II : the Jedi regex
Yes, it is intended to give emphasis :)...
Posted Of Go, C, Perl and fastq file conversion Vol IV : gone in 60 seconds (or less) to chrisarg
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…
Posted Of Go, C, Perl and fastq file conversion Vol III : pledging allegiance to the flag to chrisarg
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…
Posted Of Go, C, Perl and fastq file conversion Vol II : the Jedi regex to chrisarg
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…
Posted Of Go, C, Perl and fastq file conversion Vol I : intro to chrisarg
Next Generation Sequencing cost of experiments have dramatically declined. NGS decipher the identity (base composition, the sequence of letters in the alphabet of DN…
Posted Using Perl to prepare sequencing files to submit to NCBI's GEO to chrisarg
In the middle of a manuscript submission that requires sequencing data to be uploaded to NCBI's Gene Expression Omnibus.
Commented on open invitation to participate in Perl-OpenMP on Github
This is absolutely so cool...
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