Add Downloading Results Files

[ptth222]

There are around 1000 analysis files out of 4000 that don't have METABOLITES and DATA sections. They instead have a RESULTS_FILE. It needs to be downloaded separately from the MWTAB file. In the MWTAB specification the file is supposed to be a tab-delimited .txt file with the sample information. There is nothing about metabolite information being in this file in the specification, and the few that I have looked at do not contain any metabolite information, even though those sections are missing from the MWTAB file.

The download URL looks similar to downloading MWTAB files though, so at least that part should not be too difficult:
https://www.metabolomicsworkbench.org/studydownload/ST000071_AN000111_Results.txt

The specification does not specify that the files must be named like "ST000071_AN000111_Results.txt", so relying on that to create the URL is probably not a good idea. I think we are going to have to download the analysis file and parse it to get the results file out of it.

I am wondering if we should modify the MWTAB file and just put the results file info in there where it should be.

[hunter-moseley]

Yes, the plan is to augment the mwtab file with a metabolites block.

…

On Wed, Feb 12, 2025, 3:44 AM ptth222 ***@***.***> wrote: There are around 1000 analysis files out of 4000 that don't have METABOLITES and DATA sections. They instead have a RESULTS_FILE. It needs to be downloaded separately from the MWTAB file. In the MWTAB specification the file is supposed to be a tab-delimited .txt file with the sample information. There is nothing about metabolite information being in this file in the specification, and the few that I have looked at do not contain any metabolite information, even though those sections are missing from the MWTAB file. The download URL looks similar to downloading MWTAB files though, so at least that part should not be too difficult: https://www.metabolomicsworkbench.org/studydownload/ST000071_AN000111_Results.txt The specification does not specify that the files must be named like "ST000071_AN000111_Results.txt", so relying on that to create the URL is probably not a good idea. I think we are going to have to download the analysis file and parse it to get the results file out of it. I am wondering if we should modify the MWTAB file and just put the results file info in there where it should be. — Reply to this email directly, view it on GitHub <#12>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEP7B7H2MYM2DCNWJKWP7T2PMCVPAVCNFSM6AAAAABW7ATCMCVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2DONJVGAYTOOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>