export BSgenome directly in gzipped fasta
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@timotheeflutre-6727
Last seen 2.4 years ago
France

I would like to save a BSgenome object into a gzipped file in the fasta format. However, the following attempts didn't work.

Pass a connection opened by gzfile:

> export(object=BSgenome..., con=gzfile("~/test.fa.gz", "w"), format="fasta")
Error in .local(object, ...) : Connection resource requested as a path

Pass nothing to the con argument to retrieve a character vector that will then be written using gzfile:

> test = export(object=BSgenome.Vvinifera.URGI.IGGP12Xv2, format="fasta")
Error in .local(object, ...) : Connection resource requested as a path

Of course, I could first do export(BSgenome.Vvinifera.URGI.IGGP12Xv2, "test.fasta") and then use gzip on the cmd-line. But I'd prefer to do it all inside R.

bsgenome gzip fasta • 1.0k views
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@jeff-johnston-6497
Last seen 3.8 years ago
United States

This seems to work:

library(BSgenome.Dmelanogaster.UCSC.dm3)
export(Dmelanogaster, "dm3.fasta.gz", compress=TRUE)

 

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