[EMBOSS] density

ajb at ebi.ac.uk ajb at ebi.ac.uk
Thu Oct 23 09:09:05 UTC 2008


So it's a limitation of the web interface which requires
all graphs to be called 'graph' ?

If I've understood you correctly then, attached, are two new
versions of density.c and density.acd that only use one
graph (called 'graph') with the -dual and -quad qualifiers
working as before. I'll consider adding this to CVS. It
is, of course, currently not tested that well. Please let
me know how it behaves.



> Sorry,
> the service, which provides EMBOSS tools as web interface, fails to
> interprets properly the density ACD file.
> Everything is fine in the ACD.
>> Hi,
>> colourps and cps are synonymous so you should be able to use either.
>> If you want to specify the output type from the command line
>> you could type:
>>   density -quad -qgraph=colourps inputsequence
>> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
>>   density -dual -dgraph=cps inputsequence
>> or am I misunderstanding your question?
>> HTH
>> Alan
>>> Hi,
>>> According to the ACD file, the density application seems to use the
>>> 'graph' qualifier.
>>> When used, I get this error message:
>>> Unknown qualifier -graph=colourps
>>> graph seems to have been replaced by ggraph and dgraph.
>>> And colourps seems to be cps now.
>>> How to fix it in the source ?
>>> Thanks
> --
> Sébastien Moretti
> SIB EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4056/4221
> http://ch.embnet.org/  http://myhits.vital-it.ch/
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