individual metafile metadata: "no id column"

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Mariana Augsten

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Apr 4, 2022, 11:07:35 AM4/4/22
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Hi everyone.
I`m a new user to this DartR package. I`m so happy that it exists, I believe it will help me a lot.
Getting to the point: Trying to create my genlight object :
gl <- gl.read.dart("Report_DTb21-6643_SNP_2.csv", ind.metafile = "metadata backup.csv")

I get this message:

Adding individual metrics: metadata backup.csv .
Error in utils.dart2genlight(dout, ind.metafile = ind.metafile, probar = probar,  :
  Fatal Error: There is no id column

But I can garantee you my file has a id column, the first one, including I`ve checked that it is just the same as my SNP csv file. I`ve changed the table in so many ways, adding columns, excluding columns, only letting id and pop columns.. I dont know what else to do.

Any ideia what could be happening?
Regards, 

Mariana

Jose Luis Mijangos

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Apr 4, 2022, 7:14:38 PM4/4/22
to dartR
Hi Mariana,

Maybe you don't have the latest version of dartR. Also you can check how an individual metadata file looks like. Can you try the following code:

# Install the latest version of dartR (v2)
install.packages("dartR")
library(dartR)
# check how the individual metadata file should look like
test_csv <- read.csv(system.file('extdata','testset_metadata.csv', package='dartR'))
test_csv
# read files
dartfile <- system.file('extdata','testset_SNPs_2Row.csv', package='dartR')
metadata <- system.file('extdata','testset_metadata.csv', package='dartR')

gl <- gl.read.dart(dartfile, ind.metafile = metadata, probar=TRUE)

Cheers,
Luis

Peter Unmack

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Apr 6, 2022, 9:30:30 AM4/6/22
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occasionally there is a weird quirk where a csv file which has the term
"id" in the first cell gets treated by excel as a different file type.

See https://www.journeybytes.com/fix-csv-sylk-error-in-excel/

Double check in a plain text editor that there isn't anything else
unexpected in the file and/or copy and paste it to a new text file and
save it, rename it as csv and see if that works.

I seem to recall having this problem once in the past.

Cheers
Peter



On 5/04/2022 1:07 am, Mariana Augsten wrote:
> Hi everyone.
> I`m a new user to this DartR package. I`m so happy that it exists, I
> believe it will help me a lot.
> Getting to the point: Trying to create my genlight object :
> gl <- gl.read.dart("Report_DTb21-6643_SNP_2.csv", ind.metafile =
> "metadata backup.csv")
>
> I get this message:
>
> Adding individual metrics: metadata backup.csv .
> Error in utils.dart2genlight(dout, ind.metafile = ind.metafile, probar =
> probar,  :
>   Fatal Error: There is no id column
>
> But I can garantee you my file has a id column, the first one, including
> I`ve checked that it is just the same as my SNP csv file. I`ve changed
> the table in so many ways, adding columns, excluding columns, only
> letting id and pop columns.. I dont know what else to do.
>
> Any ideia what could be happening?
> Regards,
>
> Mariana
>
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Brianna Coulter

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Nov 24, 2022, 8:44:28 PM11/24/22
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Thank you Peter,

I was suddenly getting this problem out of nowhere. Relocated my 'id' column to the last column and it worked.

Bernd.Gruber

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Nov 25, 2022, 12:52:05 AM11/25/22
to da...@googlegroups.com

Hi

 

I saw this behaviour when you save (by mistake) the excel as an utf-8 csv (not a pure csv file). Then the first character in the csv file gets replaced by some funky character.

 

 

Maybe that is the issue here…

 

Cheers,Bernd

 

 

 

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