[EMBOSS] extractfeat and "-join" option

[Peter Rice]

Andres Pinzon wrote:
> Hi everyone,
> The following line, should return a single fasta file with all the CDS
> in a single sequence:
> 
>  extractfeat environmental:DP000238 -type CDS -join stdout
> 
> Instead it is returning each of them as a separate entry. Am I doing
> something wrong?

The -join option combines all exons for one CDS (so that it can be
translated as a complete reading frame).

It is not intended to join all CDSs into one.

for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per
exon) without -join.

Hope this helps,

Peter