[EMBOSS] Seqall Datatype
peter.robinson at t-online.de
Thu Dec 20 17:00:38 UTC 2007
Peter Rice wrote:
> 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.
thanks for the tip, that was just what I needed!
best wishes for the holidays!
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