Dear Ivaylo and Peter,
On 24/08/2012 15:59, Peter Cock wrote:
On Fri, Aug 24, 2012 at 3:46 PM, Ivaylo Stoimenov
<ivaylo.stoime...@gmail.com> wrote:
Hi,
I was wondering if it is possible for eprimer32 to read a sequence from a
string. The default input is from a file, but I need to feed primer3 from a
string, which is changing in the body of my program. Any help will be
appreciated.
Many EMBOSS tools will take a sequence on the command line
using the pretend file format "asis" (as is), or can read from stdin.
Because in this case EMBOSS is wrapping primer3, that may not
be possible - but worth checking.
Good idea to be careful - some (EMBASSY) wrappers pass the input file
name directly but eprimer32 does read the sequence and then send it to
primer3 as a string.
Any EMBOSS sequence input can be in the form asis::atcgatcgtagctgac
which simply says the string is the sequence (rather than the file
name). As the sequence has no name you can add:
-sid myseqname
to the command line which is then used in the output, and is also used
to create the default output filename of myseqname.eprimer32
The only limit will be the length of command line you are allowed on
your system, so long sequences may fail. But that is a system (shell)
limit - EMBOSS will read any length of sequence that is passed to it
this way.
regards,
Peter Rice
EMBOSS Team
_______________________________________________
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
