[emboss-dev] PHYLIP(NEW) and stdout

Peter biopython at maubp.freeserve.co.uk
Wed Sep 16 23:23:37 UTC 2009

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.

cat tiny.phy | fseqboot -reps 3 -filter

I've just found fdnadist has the same problem, in addition to the
distance matrices (the actual output) progress messages are also
printed to stdout (when using the -filter or -stdout arguments). e.g.

cat opuntia.fasta | fdnadist -method k -filter
fdnadist -sequence opuntia.fasta -method k -stdout -auto
fdnadist -sequence opuntia.fasta -method k -filter

I presume this is symptomatic of all the PHYLIPNEW tools, which is a
shame as it prevents piping their output together which to me is the
natural way to use these tools (rather than messing about with named
temporary files). It also spoils my plans for calling the PHYLIP tools
from Python and capturing their output via stdout (again, without
messing about with temp output files).

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.

If no one other than me has asked about this, perhaps it isn't a big
issue for most EMBOSS+PHYLIP users?


Peter C.

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