Test piping through non-R parsers (/exex/{gb2gff,seq-len}) on non-linux systems

thackl / gggenomes

A grammar of graphics for comparative genomics

https://thackl.github.io/gggenomes/

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Test piping through non-R parsers (/exex/{gb2gff,seq-len}) on non-linux systems #36

Open thackl opened 3 years ago

thackl commented 3 years ago

read_seqs(".fna/.gbk/.gff") and read_gbk() use non-R parsers to preprocess the data before reading them into R. This is just done by turning the file argument provided to the read_* function ("foo.fna") into a connection ala pipe("/path/to/seq-len foo.fna"). This should work on linux systems, but probably not on Windows, and I'm not sure about MacOS...

iimog commented 3 days ago

As you suspect, it did not work on Windows (at least on the Winbuilder systems of CRAN). read_seqs is now implemented in R, so this is no longer an issue. read_gbk still calls the perl script and thus, does not work on vanilla Windows.