Staden scripting

jkb at jkb at
Wed Jul 4 11:47:58 EST 2001

In <3B404922.EAC79109 at> simon andrews <simon.abdrews at> writes:
> I'm not actually doing any error checking within the Tcl script. The
> input to the script is verified by the calling Perl script, but is there
> anything else I should be checking that I can't catch externally?  I
> noticed in the script output that some sequences were failing to be put
> into the assembly.  I know there will be some duplicates, and these
> appear to give a different error message.  The tests that I have run

I expect it's just sequences which match, but not perfectly. This is the
difference between the "enter all readings" parameter in the GUI. When set to
false, sequences which match, but not well enough, are rejected. The
expectation is that you'll delay entering these until all the sequences have
been tried, and then you'll try entering them again.

The alternative (enter all) is to put such sequences in a new contig instead,
just as if they hadn't matched at all.

For more details, see:


James Bonfield (jkb at   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

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