Custom SSL format not correctly defined Mike S  2019-04-04 11:40
 

Hi,

Just a heads up that the custom ssl format described here: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec input and output file formats is not followed, at least not in Skyline 64-bit build 4.2.0.19009

For instance, that page says the header should be "file" and BlibBuilder says it needs to be "filename". Also, that page says "retention-time" is optional, but BlibBuilder says the column "RT" is required.

-Mike
 
 
Matt Chambers responded:  2019-04-04 14:09

Hi Mike,

Can you clarify where you're seeing "BlibBuilder" say it needs "filename" and "RT"? The BiblioSpec source code currently expects "file" and "retention-time" and I can't see any SslReader.cpp revision where filename or RT are expected instead.
 
Mike S responded:  2019-04-04 16:08

Sorry, I found the problem. The custom file had the extension ".tsv" and was being read as different format. Once I changed it to ".ssl", it read it just fine. Maybe it could be made more clear, particularly for the generic tab separated format files, to use the generic format, the file has to have an .ssl extension.

Thanks,
-Mike
 
Matt Chambers responded:  2019-04-05 07:17

Good point. I've updated the input/output formats page to mention the ssl file must end with the '.ssl' extension, added 'OpenSWATH .TSV' to the list of supported BiblioSpec formats linked from that page, and will update the TSV parser code to ask 'Is this an OpenSWATH TSV file?' when the columns it expects aren't found.