translate tools

[Rodrigo Lopez]

Yes, I see the problem...Good to have some more specs to go by....
The closest I can get at helping is something like:

transeq emblcd:hscfo\* -auto -frame 6 | checktrans -filter -auto -orfml 200

but that would require some post-processing to find out which orf is the
longest one and then rerun transeq/sixpack to get it explicitly. A perl or a
sh/csh script could do that. However, the correct approach is like you say:
to have an option for '-onlylargest/-onlylongest'..

R:)

> -----Original Message-----
> From: owner-emboss at hgmp.mrc.ac.uk
> [mailto:owner-emboss at hgmp.mrc.ac.uk]On Behalf Of Marc Logghe
> Sent: 03 April 2003 10:32
> To: 'Rodrigo Lopez'
> Cc: Emboss (E-mail)
> Subject: RE: translate tools
>
>
> Hi Rodrigo,
> >
> > sixpack spring to mind.
> >
> I had the same problem a few days ago. Used getorf for that with
> minsize set
> to 3000. But this was done on only one sequence for which I knew
> the size of
> the translation I needed.
> You can not do this if you don't know beforehand the value to set minsize
> to.
> This also counts for sixpack (and checktrans afaik): you can only pass a
> minsize argument. There should exist something like -only -largest.
> So I think Zhiqiang Ye's problem persists.
> Regards,
> Marc
>
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> Marc Logghe, Ph.D.
> Senior Scientist
> Scientific Computing Group
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