Open GoogleCodeExporter opened 8 years ago
Hi Alexie,
Thank you very much for using InterProScan 5.
I can imagine what you try to achieve. My guess is you would like to integrate
InterProScan into your pipeline and you want to pass the STDOUT to your next
step. You could in theory hack the bash script (interproscan.sh) to make usage
of STDIN, but I am afraid InterProScan 5 is not able to write to STDOUT as it
is configured at the moment. But we will discuss your point internally. In
theory it should be possible, but only by expanding/changing the code.
That's true in theory you could use the XML file to convert it into any other
format of your interested. But there are limitations, for instance XML result
file you've got from a nucleotide sequence analysis you can only convert into
GFF3 as it contains trace back information as well.
Unfortunately there is no mode in InterProScan 5 integrated at the moment you
can run to convert XML files, but we will discuss that point internally as well.
Kind regards,
Maxim
Original comment by Maxim.Sc...@gmail.com
on 19 Feb 2013 at 11:33
I'll handle this one.
Original comment by nuka....@gmail.com
on 6 Aug 2013 at 4:07
Original comment by Maxim.Sc...@gmail.com
on 15 May 2014 at 9:11
Original comment by Maxim.Sc...@gmail.com
on 15 May 2014 at 9:13
Original issue reported on code.google.com by
alpa...@gmail.com
on 11 Feb 2013 at 12:15