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

David Bauer david.bauer at bayer.com
Tue Jun 4 09:39:21 UTC 2013


one solution for just the longest ORF would be: 

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

-----Ursprüngliche Nachricht-----
Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Chevreux, Bastien
Gesendet: 04 June 2013 10:29
An: emboss at 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.


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