Handling EST sequences

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue Jun 29 07:47:35 EST 1999


In article <1YA*ofI3n at news.chiark.greenend.org.uk> Tim Cutts <timc at chiark.greenend.org.uk> writes:
>One of the Staden package's huge strengths is in automation.  Almost
>all of the functionality of gap4 is available through the tcl
>interface to it, stash, although there are some missing things.  For
>instance gap4's "shuffle pads" feature is not available through the
>tcl interface, and neither is "phrap reassembly".

Phrap reassembly should be available from the scripting interface as
it's just a script itself. However it's not a C-level command added to
the interpreter. See $STADENROOT/lib/phrap/phrap.tcl to see how it
works.

I agree with shuffle pads though. In theory it can be scripted, but
not without extensive work.

Thanks for your comments though. (It's nice to be appreciated.)

Cheers,

	James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



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