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
EMBOSS Team
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