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Stable Isotope Geochemistry

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Subject:
Re: IsoDat 3.0 and method name exports
From:
Sebastian Kopf <[log in to unmask]>
Reply To:
[log in to unmask]
Date:
Tue, 13 Oct 2020 12:40:48 -0600
Content-Type:
multipart/alternative
Parts/Attachments:
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Hi John,

If you are open to a programmatic solution, you can use isoreader (
https://isoreader.isoverse.org/) to export the autosampler method together
with other sequence information. In an R command line run the following
(swap out the PATH/TO/SEQUENCE/FOLDER for where your sequence results are
located). If you run into trouble, feel free to email directly.

install.packages
<https://rdrr.io/r/utils/install.packages.html>("devtools");devtools::install_github("isoverse/isoreader")

library(isoreader);
iso_read_continuous_flow("PATH/TO/SEQUENCE/FOLDER") %>%
  iso_get_file_info(select = c(Analysis, `Identifier 1`, `Identifier
2`, `AS Method`)) %>%
  write.csv("file_info_w_AS.csv")


cheers,
Seb


On Tue, Oct 13, 2020 at 5:45 AM Thomas Millican <[log in to unmask]>
wrote:

> As you pointed out, there doesn't seem to be an option for the autosampler
> method name in the items that can be exported. You could name the method
> file to reflect the autosampler method being used by its configuration and
> export the Method name, which is a Sequence Information class item. That's
> not a very elegant or proper solution though.
>
> > Greetings, list.
> >
> > Does anyone know how to export into the usual spreadsheet file (I prefer
> > .csv) the autosampler method names using IsoDat 3.0? It seems like it
> > should be a Sequence Information class column, but I don't see it. Is it
> > possible to set up as a custom identifier?
> >
>
> Tom Millican
> Research Technician
> Gulf Coast Research Laboratory
> Ocean Springs, MS
>


-- 
——————————————————
Sebastian Kopf (he/his/him)
Assistant Professor
University of Colorado Boulder
Department of Geological Sciences
[log in to unmask]
+1 (303) 735-6207
https://www.kopflab.org
https://github.com/kopflab
https://github.com/isoverse


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