[EMBOSS] eprimer32 question

Peter Rice ricepeterm at yahoo.co.uk
Fri Aug 24 16:34:55 UTC 2012

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.stoimenov at 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.


Peter Rice

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