[EMBOSS] contributing to emboss

[Peter Rice]

Hi Afif,

For you request to get the gff output without the sequence...

GFF is both a feature and a sequence format. If you run "seqret -feat" 
you are reading both sequence and feature information. You can write 
them out to two separate files by redirecting the features with the 
output qualifiers -offormat (-off) and -oufo

For example:

seqret annotatedgenome /dev/null -oufo gff:annotation.gff

or

seqret annotatedgenome /dev/null -oufo annotation.gff -off gff


Hmmm.... just noticed -off may be confusing with other programs that 
have a -offset option. I don't think any of them have feature output.

regard

Peter Rice
EMBOSS team

On 21/06/2022 23:33, Afif Elghraoui wrote:
> Thanks for the update!
> 
>  > Then the fun starts. Any suggestions for new features?
> 
> Nothing particularly fancy. What I was primarily interested in was an 
> option for seqret to not include the genome sequence in gff output.
> But overall, and maybe this is too much, I would've loved for the emboss 
> tools to be more in the unix filter style. Like if I could just
> 
>    samtools faidx gene | transeq ...
> 
> to get a translation, etc.
> 
> many thanks and regards
> Afif
> 
> On Tue, Jun 21, 2022 at 3:21 PM Peter Rice <ricepeterm at yahoo.co.uk 
> <mailto:ricepeterm at yahoo.co.uk>> wrote:
> 
>     Hi Afif,
> 
>     Yes... it is in progress. My hopes to recover the CVS server (and all
>     the individual commits) came to nothing - there was no useable backup.
> 
>     However, we do have all the old releases since the very early days,
>     So I
>     have been putting them on to github. That will give us a record of
>     every
>     release and a summary of all the changes made.
> 
>     Almost there, but I have to keep up with my tranSMART development tasks
>     too. However, the tranSMART beta release went out today, so I will soon
>     have thew final rel;ease done and some free time to catch right up to
>     the last EMBOSS release.
> 
>     Then the fun starts. Any suggestions for new features? I can start with
>     removing anything too far out of date (including some of the extra data
>     resources we added 10 years ago) and updating the external libraries.
> 
>     The github repository is at https://github.com/oryzabioinformatics
>     <https://github.com/oryzabioinformatics> (but
>     wait for the 6.6.0 branch to appear - it is up to 6.4.0 so far, so
>     nearly there)
> 
>     regards,
> 
>     Peter Rice
> 
>     On 21/06/2022 22:23, Afif Elghraoui wrote:
>      > Hello,
>      > I saw an old message on the -dev list that there was some
>     migration to
>      > github in progress:
>      >
>     https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html
>     <https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html>
> 
>      >
>     <https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html
>     <https://mailman.open-bio.org/pipermail/emboss-dev/2018-January/001502.html>>
> 
>      >
>      >
>      > Did anything ever happen with that?
>      >
>      > thanks
>      > Afif
>      >
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