Dear Peter,
I am trying my hand at an EMBOSS program and would like to read in a
list of sequences from a FASTA file and make pairwise comparisons
between each sequence. If I startwith a AjPSeqall object
AjPSeqall seqs=NULL;
seqs = ajAcdGetSeqall ("seqs");
You want all the sequences in memory so you can work through the pairs -
better to use AjPSeqset and ajAcdGetSeqset
in the documentation, but I would like to do something like a double for
loop to get all pairwise comparisons. What is the best way of doing
this? I have been searching in the online docs but did not yet find
anything.
distmat has the kind of loop you are looking for (except it does self
matches too)
By the way, in http://emboss.sourceforge.net/developers/program.html
these datatypes are flagged as obsolete by the compiler, so the document
may need revision here?
Yes, all being revised for the books we are preparing ... we will take a
look through program.html and make some basic updates to correct these
things.
regards,
Peter
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
