Hi Peter and Peter, Many thanks to both of you for the valuable help. It is very important for me to have as less file-related operations as possible, and passing a string helps to reduce the input from files. I wondered if it is possible to hijack the output of Primer3 to some sort of object directly to eprimer32 without writing to a file and thus making Primer3 sort of a function to an external program. I am aiming of running a validation cycle for the primers suggested by Primer3 and if necessary to change the input to Primer3 until certain criteria are fulfilled. Therefore I would like to skip a file-write-read operation until everything is optimal. Do you know if that is still possible, or I always need to read from Primer3 output files.
Kind regards, Ivaylo 2012/8/24 Peter Rice <ricepet...@yahoo.co.uk> > 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