-osformat strangeness

[Peter Rice]

Gary Williams writes:

>Can anyone explain this behaviour? When I use '-osf staden' or '-osf
>gcg' I get no output but no error messages.

Strictly, this happens when '-ossingle' is on. This forces output to
go to a separate file for each sequence, and is turned on for formats
that do not support multiple sequences in one file (GCG/GCG8,
STADEN/EXPERIMENT, RAW/TEXT/PLAIN)

Any other format with -ossingle on the command line will do the same.

GCG and STADEN with -noossingle will write to the same file. For GCG
format EMBOSS is able to read the resulting file (but GCG cannot :-)

This behaviour could be changed, but needs some careful planning.  For
example, with one output file you may want it to be used. With many
output files you may want them all to be automatically named.

Perhaps some special processing for stdout and stderr would be useful,
and for user-defined output filenames the user's choice could at least
be used for the first sequence (maybe with a warning for the second
sequence if there is one).

So many cases to consider. All packages that write GCG format face
these kinds of problems.

Peter

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
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Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/