[R] Convert CSV file to FASTA

[Mike Marchywka]

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> Date: Wed, 31 Aug 2011 01:36:51 -0700
> From: oliviacreemer at gmail.com
> To: r-help at r-project.org
> Subject: [R] Convert CSV file to FASTA
>
> Hi there,
>
> I have large excel files which I can save as CSV files.
>
> Each excel file contains two columns. One contains the chromosome number and
> the second contains a DNA sequence.
>
> I need to convert this into a fasta file that looks like this
> >chromosomenumber
> CGTCGAGCGTCGAGCGGAGCG....
>
> Can anyone show me an R script to do this?
>

If you can post a few lines of your "csv" someone can probably give you a bach
script to do it. It may be possible in R but sed/awk probbly work better. IIRC, fasta
is just a name line followed by sequence. If your csv looks like "name, XXXXXXXXXX"
it may be possible to change comma to space and use awk with something like print ">"$1"\n"$2 
etc.



> Many thanks
>
> x
>
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