[Seqinr-forum] read.fasta error

[Jean Lobry]

Hi Mat,

as a defensive trick you can use seqinr::read.fasta() to make
sure to call the read.fasta() function from seqinr.

Best,

JLO

Le 06/10/2016 à 16:49, Beale, Mat a écrit :
> Ooops, sorry for bothering people.  I had another enviromental function
> loaded called read.fasta that was messing things up.
>
> ------------------------------------------------------------------------
> *From:* seqinr-forum-bounces at lists.r-forge.r-project.org
> <seqinr-forum-bounces at lists.r-forge.r-project.org> on behalf of Beale,
> Mat <mathew.beale at ucl.ac.uk>
> *Sent:* 06 October 2016 15:09:42
> *To:* seqinr-forum at lists.r-forge.r-project.org
> *Subject:* [Seqinr-forum] read.fasta error
>
>
> Hi All,
>
>
> Has anyone noticed any strange behaviour with read.fasta since the
> update to v3.3.1?  I have a number of long-term scripts (running on
> various clusters and locally) that until recently all worked very
> nicely.  I revisited my scripts this week only to find error messages
> during the read.fasta stage:
>
>
> wgsconsensus <-read.fasta(file=consensusfile,as.string=F,
> seqtype=c("DNA"),seqonly=F,set.attributes=F) # consensusfile is just the
> path to fasta
>
>
> Error in read.fasta(file = consensusfile, as.string = F, seqtype =
> c("DNA"),  :
>   unused arguments (as.string = F, seqtype = c("DNA"), seqonly = F,
> set.attributes = F)
>
> I've encountered this on different platforms, running the latest (and
> older versions) of R, and with both new files and those I've run before.
>  Sequential removal of arguments hasn't been particularly informative,
> and running it without any arguments also doesn't help:
>
>
> read.fasta(file=consensusfile)
> Read 2 items
> Error in seqs[[i]] : subscript out of bounds
>
> Can anyone advise what is happening?  Have I just made a silly error?
>
>
> Many thanks,
>
>
> Mat
>
>
>
>
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