[Bioperl-l] Bio::Seq::SequenceTrace and Bio::SeqIO::scf

[Tony Cox]

On Wed, 29 Jan 2003, nkuipers wrote:

+>>The creation of the SequenceTrace object required that SeqIO::scf be
+>>rewritten.  I gladly did this because the old module was somewhat...
+>>clunky.
+>
+>I see from a recent message that Tony Cox also "tweaked" SeqIO::scf.  Perhaps
+>the two of you should give a look-see at each other's modifications, if you
+>haven't already.

I just looked at the changes anf they don't confict with anything I have except
my proposed change to the way the filehandles are used if it is a String::IO
handle. I havn't committed these yet anyway - I'm trying to hunt down a 5.004
installation to test it on.

Chad's stuff looks good to me. I'm curious as to why you might want to emulate a
chromatogram in an scf file.

The trace slice looks useful but I'm not sure whether one can use it to slice a
"real" scf file, or only for home-made /emulated ones.  Trimming real files
would be v. useful for me since I have already written code to do this the long
way while rendering multi-trace assemblies anchored about a single basepair.

I was seeing a problem with an off-by-one error in the SWQ module but I havn't
tracked it down yet to either my code or the SWQ module.

cheers

Tony


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