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Bio::Tools::CodonTable is out of date (again) #391

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carandraug opened this issue Apr 25, 2024 · 2 comments
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Bio::Tools::CodonTable is out of date (again) #391

carandraug opened this issue Apr 25, 2024 · 2 comments

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@carandraug
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The code in CodonTable is from 2017. It is is missing a few codon table 32, some amino acids changed in table 27-30, table 3 has a new start codon, table 14 has less 6 start codons and less one stop codon. I will update the code for te last version (current version is 4.9)

Issue #389 was about missing codon table 15 which was added recently. Issue #256 was in 2017 about needing to update the codontable code which at the time reflected the version from 2013. Maybe it makes sense to parse the official release instead of manually updating it but the source is ASN.1 in value notation format and I can't find a parser for it anywhere.
carandraug added a commit that referenced this issue Apr 25, 2024
@carandraug
Bio::Tools::CodonTable: update data from versino 4.2 to 4.9 (#391)
e2273cd
@carandraug
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I've written a naughty parser and updated the code based on the current version of gc.prt in commit e2273cd. To make this easier, I'm thinking of simply including the gc.prt in the __DATA__ section of the module and have it parsed at the start.

carandraug added a commit that referenced this issue Apr 26, 2024
@carandraug
Bio::Tools::CodonTable: include and parse the gc.prt file (#391)
a73febe 
To make it simpler to keep things up to date, just include the gc.prt
(the NCBI data file of codon tables in ASN.1 print format) below
__DATA__ and parse it.  The file is very small and parsing it is very
quick.

We can't read DATA in a BEGIN block so this also changes the BEGIN
into a INIT block.  I'm not sure why the code there needs to be inside
them though.
@carandraug
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I've pushed a73febe which includes the contents of gc.prt below __DATA__ and have the module parse it when it starts. Closing this as fixed.

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@carandraug