Re: [EMBOSS] is it possible to use emboss without writing a full application?
Hi Jeff, Further to Peter's email, i have checked the needle inputs that only the sequence and the matrix parameters are emboss specific types. You can set your sequence inputs using the ajSeqNewNameC function which use basic C types. AjPSeq ajSeqNewNameC(const char* txt, const char* name) First parameter is the text of the input sequence. If you are not aligning one sequence with multiple sequences than the algorithm can be simplified, such as you can delete the while-loop and the seqall parameter. For the matrix parameter you can use the ajMatrixNewFile function as in the following example. ajMatrixNewFile(ajStrNewC(/myembossinstall/share/EMBOSS/data/EBLOSUM80)) If you are doing many alignments and not using the end gap penalties you may consider using the emboss stretcher program instead. stretcher uses a more advanced algorithm, its memory consumption is less and also it is sometimes faster than needle. --mahmut I have a completely different way of gathering command-line user input that doesn’t use Ajax/ACD, can I still use emboss for sequence alignment? That’s the kind of example I need. ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
[EMBOSS] is it possible to use emboss without writing a full application?
EMBOSS Community, I’ve looked at the example application “seqret” and I think I understand it well enough. However, I am more interested in being able to programmatically call the “needle” application without a system call. More specifically, I would like to simply use emboss’s NW alignment function *without* writing a full application. I guess another way to ask this is, I have a completely different way of gathering command-line user input that doesn’t use Ajax/ACD, can I still use emboss for sequence alignment? That’s the kind of example I need. Any help is appreciated. Thanks. ___ Jeff Daily Scientist DATA INTENSIVE SCIENTIFIC COMPUTING GROUP Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K7-90 Richland, WA 99352 USA Tel: 509-372-6548 Fax: 509-372-4720 jeff.da...@pnnl.gov www.pnnl.gov ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] is it possible to use emboss without writing a full application?
On 04/04/14 14:30, Daily, Jeff A wrote: EMBOSS Community, I’ve looked at the example application “seqret” and I think I understand it well enough. However, I am more interested in being able to programmatically call the “needle” application without a system call. More specifically, I would like to simply use emboss’s NW alignment function *without* writing a full application. I guess another way to ask this is, I have a completely different way of gathering command-line user input that doesn’t use Ajax/ACD, can I still use emboss for sequence alignment? That’s the kind of example I need. Any help is appreciated. Thanks. Yes, you can create sequences and other datatypes from a string (which is basically what ACD does internally) and simply call the setup functions if you need, for example, the EMBOSS database handling enabled. You will find the functions you need in ajax/acd/ajacd.c Let us know if you need any further help. Maybe some of the functions do not work ideally in a standalone mode - we have not tried them that way since the early versions but, by design, it should be straightforward to do. regards, Peter Rice EMBOSS Team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
