You read the biopython code here? That's the best explanation of the quality scores I've seen.

There's also a nice text-graphic about 2/3rd's of the way down the wikipedia page

Finally, FastQC guesses the encoding of your quality scores, so you could look at the java code.

Here is a Perl script for guessing the quality scale

https://www.uppnex.uu.se/content/check-fastq-quality-score-format

Does the FAST-X toolkit answer your needs ? http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_quality_boxplot_usage

I wrote a Python-based FASTQ quality guesser: https://github.com/DarwinAwardWinner/fastqident It uses BioPython's FASTQ parser, so it will work on anything that is parsable by BioPython.

Isn't that solving the wrong problem? The guessing code in FastQC looks fragile, it simply looks at the smallest code used for qualities, so it depends on actually seeing low quality bases.

I believe you should get the correct encoding from extra knowledge (i.e. knowing which version of which program generated the file, say from some log file), and then convert to a well specified format (e.g. BAM) once. Please don't perpetuate the practive of guessing at the details underspecified formats.

In addition to Ryan, I have a python based fastq quality guesser as well if you would like to use it. It is just standard python (no biopython). PM if interested.