[adegenet-forum] error "Miss-formed strings in replacement"

[Jombart, Thibaut]

Hello, 

yes indeed, this is a bug, the function does not expect entirely non-typed loci. 

If RAM is not a constraint (if your dataset is small), you don't have to use genlight. You can use DNAbin format; to read data in:
dna <- fasta2genlight("sequ.fa")

Cheers
Thibaut

________________________________________
From: Gabriel Terraz [gabriel.terraz at univ-lyon1.fr]
Sent: 08 February 2013 14:51
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] error "Miss-formed strings in replacement"

Here is a dataset (attached file):
(My whole dataset are numerous file with small dataset like this one)

 >ana
CAGGTGACG-CAATTTTACTGTAATTTGTTTGGCCGCACGTAC---TTGGAGGCCT-GACATGGGGCAATGTCAGCTCGTTTGTGCATGCTCAG-------
 >ere
CAGGTGACG-CAATTTTACTGTAATTTGTTTGGCCGCACGTAC---TTGGAGGCCT-GACATGGGGCAATGTCAGCTCGTTTGTGCATGCTCAG-------
 >sec
CAGGTGACG-CAATTTTACTGTAATTTGTTTGGCCGCACGTAC---TTGGAGGCCT-GACATGGGGCAATGTCAGCTCGTTTGTGCATGCTCAG-------
 >vil
CAGGTGACG-CAATTTTACTGTAATTTGTTTGGCCGCACGTAC---TTGGAGGCCT-GACATGGGGCAATGTCAGCTCGTTTGTGCATGCTCAG-------

Thanks a lot

Gabriel Terraz  -Doctorant-


Tel: +33(0)4 72 43 29 08

Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558
Batiment Mendel
Université Claude Bernard - Lyon 1
43, Bd du 11 novembre 1918
69622 Villeurbanne

Le 08/02/2013 15:00, Jombart, Thibaut a écrit :
> Hello,
>
> can you post a (small) toy dataset to reproduce the error?
>
> Cheers
>
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Gabriel Terraz [gabriel.terraz at univ-lyon1.fr]
> Sent: 08 February 2013 13:01
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] error "Miss-formed strings in replacement"
>
> Hello,
> I am encountering a problem with the fasta2genlight function:
> Here is the error it gives me:
>
>
> Erreur dans `alleles<-`(`*tmp*`, value = list()) :
>     Miss-formed strings in replacement (must be e.g. 'c/g')
>
>
> It seems that the error is due to SNPs absence in the data file.
>
> Does someone already encountered this error ?
>
> Thanks for your help,
>
> Gabriel
>
>
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