Dear all, not sure if this is feasible but one would think it should… I'd like to automate the creation of making transcript database from gff3/gtf files taken from ftp server without having to download the annotation. Some of the files (most likely all of them) would be compressed and would require decompression in line.

I tried using gzcon on a connection and passing it to the makeTranscriptDbFromGFF() function unsuccessfully. Her is a toy example:

gff.file <- "ftp://ftp.ensemblgenomes.org/pub/fungi/current/gff3/schizosaccharomyces_pombe//Schizosaccharomyces_pombe.ASM294v2.20.gff3.gz"
txdb <- makeTranscriptDbFromGFF(gzcon(url(gff.file)),"gff3")

However, the gff3 file can be loaded and stack in memory by
in.mem <- readLines(gzcon(url(gff.file)))

But using read.table() fails with the same error as the makeTranscriptDbFromGFF()
in.mem.2 <- read.table(gzcon(url(gff.file)))

So, I suspect that the issue is the mode of the conniption that is set to binary that triggers the pushBack error. Must be some way to bypass that.

Anyhow, having the ability to pass a connection to the  makeTranscriptDbFromGFF() function would be really useful.

Thanks


--  Marco Blanchette, Ph.D.
Genomic Scientist
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110
www.stowers.org


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