[EMBOSS] DNA sequence as input argument
pmr at ebi.ac.uk
Fri Feb 11 11:11:13 UTC 2011
On 11/02/2011 10:54, Sigve Nakken wrote:
> 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?
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:
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
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