[emboss-dev] PHYLIP(NEW) and stdout

[Peter Rice]

Peter C. wrote:
> Hi all,
> 
> Some years ago I filed bug 1587853 about fseqboot including "noisy"
> output on stdout, which means it can't be used for bootstrapping where
> the resampled alignments are sent to stdout (e.g. using the -filter or
> -stdout arguments). e.g.
>
> Would it be simple to make all these progress messages go to stderr
> instead of stdout? Or just disable them if -stdout or -filter has been
> used? I can appreciate that as you are wrapping a 3rd party tool here,
> any EMBOSS specific changes should be kept to a minimum, so this
> may not be that simple.

Yes ... the phylip code is pretty clean and we could put something in to 
catch these messages with stdout as the default but some other output 
available as a command line option.

I just added the phylip 3.69 code changes in CVS. I will look into this 
when I am back next week.

regards,

Peter