Re: [EMBOSS] getorf: propose new switch '-longest'

[Peter Cock]

On Tue, Jun 4, 2013 at 9:29 AM, Chevreux, Bastien
bastien.chevr...@dsm.com wrote:
 Hi there,

 in case someone goes over 'getorf' for a next revision: I propose to
 add a switch like '-longest' to retrieve the longest potential ORF per
 sequence. Maybe also something like '-grace PERCENT' which - in
 combination with '-longest' - would retrieve the longest ORF and all
 ORFs which are up to PERCENT smaller than the longest one.

 Best,
   Bastien

Good idea - I was just going over my Galaxy getorf equivalent
and comparing it - at the time I may have forgotten the EMBOSS
getorf had a Galaxy wrapper:

http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss

One major differences is my script does have a longest mode -
actually three modes to offer some choice in the tie breaker
situation where there are multiple equally long ORFs:

* All ORFs/CDSs from each sequence
* All ORFs/CDSs from each sequence with the maximum length
* First ORF/CDS from each sequence with the maximum length

This was written specifically as a way to quickly pull out probable
coding sequence from transcriptome assemblies (as amino acids
or nucleotides) where for simplicity I just wanted the longest
candidate protein sequence.

Peter C.
___
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss

Re: [EMBOSS] getorf: propose new switch '-longest'

[David Bauer]

Hi,

one solution for just the longest ORF would be: 

getorf sequence.fa  | sizeseq -filter -desc | seqret -filter -first

David.
-Ursprüngliche Nachricht-
Von: emboss-boun...@lists.open-bio.org 
[mailto:emboss-boun...@lists.open-bio.org] Im Auftrag von Chevreux, Bastien
Gesendet: 04 June 2013 10:29
An: emb...@emboss.open-bio.org
Betreff: [EMBOSS] getorf: propose new switch '-longest'

Hi there,

in case someone goes over 'getorf' for a next revision: I propose to add a 
switch like '-longest' to retrieve the longest potential ORF per sequence. 
Maybe also something like '-grace PERCENT' which - in combination with 
'-longest' - would retrieve the longest ORF and all ORFs which are up to 
PERCENT smaller than the longest one.

Best,
  Bastien

--
DSM Nutritional Products | NIC-RD / HNH Bioinformatics
Bldg. 203.4/188 | P.O. Box 2676 | 4002 Basel | Switzerland
T +41 61 815 8264



DISCLAIMER:
This e-mail is for the intended recipient only.
If you have received it by mistake please let us know by reply and then delete 
it from your system; access, disclosure, copying, distribution or reliance on 
any of it by anyone else is prohibited.
If you as intended recipient have received this e-mail incorrectly, please 
notify the sender (via e-mail) immediately.

___
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss

___
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss