Feature request: input/output vs pipes on unix system

[GoogleCodeExporter]

Hello,
It would be very useful if I could pipe a fasta file into pagan on stdin and 
get the output to stdout, since I'd like to be able to call pagan from a 
separate application without writing any temporary files.

Original issue reported on code.google.com by avi.mos...@gmail.com on 26 Nov 2014 at 2:40

[GoogleCodeExporter]

Hi,

The problem is that Pagan typically requires multiple input files and writes 
multiple output files. To me, it is foremost a method for alignment extension 
and thus requires three input files: reference alignment, reference tree and 
query sequences.

One could provide Unix-style piping for multiple alignments without guide tree 
and with Fasta output only. Are people using Pagan that way and is there really 
need for such a feature?

Regards, Ari

Original comment by ari.loyt...@gmail.com on 1 Dec 2014 at 8:42

[GoogleCodeExporter]

It might just be me.  The feature that initially drew me to Pagan was its 
ability to test both forward and reverse-complement configurations in an 
alignment.  I am presently using Muscle as part of a web tool that can perform 
sequence alignments - but this makes it most convenient to call on the server 
side, pass in dynamically selected sequences, and retrieve the output as a 
pipe.  This is likely an unusual use case.

Regards,
     -Avi

Original comment by avi.mos...@gmail.com on 2 Dec 2014 at 7:08