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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Exporting results #36

Closed ykim7263 closed 2 years ago

ykim7263 commented 3 years ago

Hi all,

Is there any way to export the results including all the results from the batch analysis? I realized that the "Writing summary" function only contains 1 compound per feature. It would be great if I can extract all the results in a single file?

mfleisch commented 3 years ago

Hey, there is no such file since the number of candidates for a single feature can be very large depending on the search database and we do not want to store these lists multiple times.

However, when writing summaries, SIRIUS will write a file named structure_candidates.tsv for each feature that contains all structure candidates of this feature. So simply concatenating them should do the job I think.

yellow-byte commented 3 years ago

How to customize the sorting of summary files, e.g. using CSI:finger's similarity calculation as the primary rule

marcus-ludwig commented 2 years ago

If I understand you correctly, you want to sort all compounds individual structure_candidates.tsv summary files by the score of the top candidate. This is nothing SIRIUS does support or is designed for. SIRIUS provides most information in easy machine-readable files (.tsv, .json). For such specific tasks, you will either have to write your own small script in a language of your choice or you may be able to perform the sorting in Excel after concatenating these summary files.