[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 



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