[maker-devel] Specify multiple files to rmlib

[Carson Holt]

No.  There are some implementation issues related to how repeats are
processed and collapsed that may cause hidden bugs with the comma separated
list, so it needs some more testing.

The label is added to the output GFF3.  For example
protein=uniprot.fasta:uniprot, would cause the gff3 label to be
protein2genome:uniprot rather than just protein2genome.  Programs like
GBrowse know how to use the labels to generate on/off check boxes to turn
just some of your protein results on/off in a viewer rather than all of
them.

--Carson



From:  Shaun Jackman <sjackman at gmail.com>
Date:  Friday, May 16, 2014 at 2:45 PM
To:  Carson Holt <carsonhh at gmail.com>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Specify multiple files to rmlib

Excellent. Thanks, Carson. Is the rmlib feature included in 2.31.5? What is
the purpose of the label? Does it affect the GFF file output by MAKER?


 
-- 
http://sjackman.ca
 

On 2014-May-16 at 13:33:23 , Carson Holt (carsonhh at gmail.com) wrote:
 
> It could be done.  I've made some changes to the subversion repository if you
> want to test it.  You should also be able to use labels just as you can with
> other comma separated lists in MAKER using ':' to separate the label.
> 
> Example --> rmlib=repeats.fasta:some_label,repeats2.fasta:another_label
> 
> I've also found the other_gff issue.  It was fixed in the subversion
> repository but not in the release package I made the other day, so I've
> updated the release to 2.31.5.
> 
> --Carson
> 
> 
> 
> 
> From: Shaun Jackman <sjackman at gmail.com>
> Reply-To: Shaun Jackman <sjackman at gmail.com>
> Date: Friday, May 16, 2014 at 11:16 AM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Specify multiple files to rmlib
> 
> Hi, Carson. Some options of maker accept multiple files as a comma separated
> list, but rmlib does not. Could it?
> 
> Thanks!
> Shaun
> 
> P.S. Any update on the fix to other_gff?
> 
>  <http://sjackman.ca> http://sjackman.ca
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