[EMBOSS] DNA sequence as input argument

Peter Rice pmr at ebi.ac.uk
Fri Feb 11 11:11:13 UTC 2011

Dear Sigve,

On 11/02/2011 10:54, Sigve Nakken wrote:
> Hi,
> Is there any way in which one can read a DNA sequence directly from the
> command line (that is
> as a string input argument) rather than from a file? I am especially
> interested in finding repeats,
> inverted repeats etc. (e.g. 'einverted', 'etandem' EMBOSS apps). Instead
> of creating a FASTA file
> for each query sequene, I would like to read the sequence directly from
> the command line. Is this possible?

seqret asis::ctgatcgatgctagctgac

the "asis" format was included exactly for this purpose. You do need to 
take care that a long sequence is not too long for your shell to handle 
on the command line (a shell issue, not an EMBOSS issue).

You can also add to the command line:

-sid abc123

This will give it an ID of abc123 and the output file will default to 
(for seqret) abc123.fasta and will have the abc123 identifier in it.

Hope this helps

Peter Rice

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