Xbap, list contigs?

Staden "R." rs at mrc-lmb.cam.ac.uk
Sat May 6 12:58:05 EST 1995


Hi,

Ive just tried xbap on our alpha and it plots ok. I can only think
that the file that defines the layout of the plots has not been read,
in which case all plot areas are zero in size and nothing gets drawn.
The file is defined as follows on my machine:
BAPMARG=/nfs/arran/home5/pubseq/share/tables/BAP.MRG
and should appear in your environment. On my machine it is set up as follows
# Staden software
setenv STADENROOT /nfs/arran/home5/pubseq/share
source $STADENROOT/staden.login

in my .login file.

If this does not solve the problem let me know.

The function "show relationships" will give lists of contigs. You can
select a contig by typing the name or number of any gel reading it contains.
Names must be preceded by /       eg /fred.seq

There are two important points to make:
1. bap was replaced by gap last year. Gap has a new database that
records a great deal of extra information about the readings and
their templates, but still has the same old user interface.

2. We are close to finishing a tcl/tk graphical interface to gap which
is radically different and we believe will be well received. It has 
plots of templates, readings etc and graphical ways of displaying many
of its results. It also has graphical tools for picking up contigs and
reordering them. This is the "final" version of our assembly program and
has taken 3 years to produce! We will be looking for groups to try it
out in the next week or so, and then if no major problems are found
(which we doubt because many of the underlying algorithms have been in
use for some time), we should be ready for general release soon after.
Then we will be converting the rest of the package to tcl/tk.

Hope this helps.

Rodger Staden



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