[EMBOSS] contributing to emboss

[David Bauer]

Hi All,

If you want the -filter as default, this can be done by setting an environment variable:
setenv EMBOSS_FILTER 1

Best,
David

-----Ursprüngliche Nachricht-----
Von: EMBOSS <emboss-bounces at mailman.open-bio.org> Im Auftrag von Kiefer, Dr. Markus
Gesendet: 22 June 2022 09:11
An: emboss at mailman.open-bio.org
Betreff: Re: [EMBOSS] contributing to emboss

Hi Afif, 

do you know about the -filter option? But I agree, that should be the default. 

I think the retrieval functionality is in need of an overhaul. There should be an easier way to access modern Genbank for example, while e.g. SRS and GCG are much less important, meanwhile. 

Best,
Markus 


Am Dienstag, dem 21.06.2022 um 15:33 -0700 schrieb Afif Elghraoui:
> 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> 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 with removing anything too far out of date (including some of the 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgi
> > thub.com%2Foryzabioinformatics&data=05%7C01%7C%7C72a0efd9df0e4e6
> > 900f108da541f4eb4%7Cfcb2b37b5da0466b9b830014b67a7c78%7C0%7C0%7C63791
> > 4791254959489%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2
> > luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=gEtD%
> > 2Bb6lD7dLhEBSWsPAKHDp%2FhiYBRvzZKJBGcBGI3o%3D&reserved=0 (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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2F
> > > mailman.open-bio.org%2Fpipermail%2Femboss-dev%2F2018-January%2F001
> > > 502.html&data=05%7C01%7C%7C72a0efd9df0e4e6900f108da541f4eb4%7C
> > > fcb2b37b5da0466b9b830014b67a7c78%7C0%7C0%7C637914791254959489%7CUn
> > > known%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik
> > > 1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=NcqCrwTbE7o90jcREVJ
> > > UIZSkB%2F%2BrTtz4bX9Ku%2BV%2BjjI%3D&reserved=0
> >  
> > > <
> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma
> > ilman.open-bio.org%2Fpipermail%2Femboss-dev%2F2018-January%2F001502.
> > html&data=05%7C01%7C%7C72a0efd9df0e4e6900f108da541f4eb4%7Cfcb2b3
> > 7b5da0466b9b830014b67a7c78%7C0%7C0%7C637914791254959489%7CUnknown%7C
> > TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJX
> > VCI6Mn0%3D%7C2000%7C%7C%7C&sdata=NcqCrwTbE7o90jcREVJUIZSkB%2F%2B
> > rTtz4bX9Ku%2BV%2BjjI%3D&reserved=0>
> > > 
> > > 
> > > Did anything ever happen with that?
> > > 
> > > thanks
> > > Afif
> > > 
> > > _______________________________________________
> > > EMBOSS mailing list
> > > EMBOSS at mailman.open-bio.org
> > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2F
> > > mailman.open-bio.org%2Fmailman%2Flistinfo%2Femboss&data=05%7C0
> > > 1%7C%7C72a0efd9df0e4e6900f108da541f4eb4%7Cfcb2b37b5da0466b9b830014
> > > b67a7c78%7C0%7C0%7C637914791254959489%7CUnknown%7CTWFpbGZsb3d8eyJW
> > > IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2
> > > 000%7C%7C%7C&sdata=mz25S7gEohZvgFdtmg1Qwj4qLOD7kL%2FJAz7dNNwB3
> > > sI%3D&reserved=0
> > 
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at mailman.open-bio.org
> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fma
> > ilman.open-bio.org%2Fmailman%2Flistinfo%2Femboss&data=05%7C01%7C
> > %7C72a0efd9df0e4e6900f108da541f4eb4%7Cfcb2b37b5da0466b9b830014b67a7c
> > 78%7C0%7C0%7C637914791254959489%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w
> > LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%
> > 7C&sdata=mz25S7gEohZvgFdtmg1Qwj4qLOD7kL%2FJAz7dNNwB3sI%3D&re
> > served=0