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lifs-tools / rgoslin

Rgoslin Repository for Bioconductor submission
MIT License
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Possible parsing error for TAGs with one specified fatty acid #31

Closed metabohaid closed 9 months ago

metabohaid commented 9 months ago

Hi,

When using Rgoslin v1.6.0 for parsing triacylglycerols where only one fatty acid is explicitly given (e.g. TG 20:1_52:1), the lipid class is recognized as diacylglycerol.

E.g. the following command will lead to the parsed results below: parseLipidNames("TG 20:1_52:1")

This behaviour is consistent across all TAGs that I have tested (ca. 500). isValidLipidName() is not complaining about the nomenclature, and in previous versions, the parsing has worked. Is this a new shorthand nomenclature or maybe a bug?

dominik-kopczynski commented 9 months ago

Hi Metabohaid,

Thank you for your message. Yes, that was a change in the shorthand nomenclature's revision that 'TG 20:1_52:1' is now partially resolved. Since rgoslin 2.x.x, this is adapted. However, we could not yet update it in the Bioconductor repository. If you want, I can offer you a pre-compiled version of rgoslin 2 with an installation instruction.

Cheers, Dominik

metabohaid commented 9 months ago

Hi Dominik, would be great if your could provide a pre-compiled version of rgoslin 2.

Thanks, Mark

dominik-kopczynski commented 9 months ago

Hey Mark, I am done. Do you need a compiled version for a Windows or a Linux platform?

metabohaid commented 9 months ago

Hi Dominik, I am using Windows, but my colleague might be interested in a Linux version. Thank you for help!

dominik-kopczynski commented 9 months ago

Hi Mark, thank you for being so patient. You can download now the manually compiled 2.0 version here [1]. Alternatively, your colleagues can clone this git repository, compile, and install the newest version on their own, the current branch is "v2_12". If they need support, please let me know. We will inform you as soon as we manage to update the Bioconductor repository.

Cheers, Dominik

[1] https://lipidomics.at/nextcloud/index.php/s/D27nizN8gzFYXtG (NFcANt!lsat4li)