[EMBOSS] Seqall Datatype
Peter Rice
pmr at ebi.ac.uk
Thu Dec 20 16:07:18 UTC 2007
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
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