September newsletter

Ed Griffiths edgrif at sanger.ac.uk
Fri Dec 1 08:20:19 EST 2000

Please find the below the long delayed September newsletter.

cheers Ed

| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk   URL: http://www.sanger.ac.uk/Users/edgrif |
|   Tel: +44-1223-494780       Fax: +44 1223 494919                      |


ACEDB User Group Newsletter - September 2000

If you want to have this newsletter mailed to you _or_ you want to make
comments/suggestions about the format/content then send an email to
acedb at sanger.ac.uk.


There have been no newsletters for too long, sorry, sorry, sorry. We have
had a number of problems with the build/test system for acedb which have
precluded the usual monthly releases of development code. This has ended up
with me delaying sending out the newsletters because there seemed little
point when they refer to new features/bug fixes in code that is not yet

General News

_Xref bug believed fixed..._ a long standing bug in xref which resulted in
"object locked" errors when trying to update databases with objects
containing particular types of xrefs has now been fixed (see bugs section).

Most news this month is about bug fixes as we get ready for the next
significant release which will be called Acedb 4_9.

New Features

tace command sets

If you issue the "?" command from within tace you get to see a list of the
commands that you can issue. Previously in tace (and aceclient) this list
was misleading because it included commands that the user would not be able
to run because they did not have write access to the database. This has now
been fixed so that if a user does not have write access they will not see
commands that require write access.

Bugs Fixed

tace bug

When tace is run via a pipe (e.g. from a perl or shell script) it saves the
database on quitting by default. This behaviour was broken in 4_8 and has
now been restored. This is particularly important because running tace via
scripts is one of the main mechanisms used at Sanger for doing large scale
updates to databases.

Expanding database

There was a problem in 4_8 with databases growing enormously when a large
number of separate updates were made to the database. This has been fixed
and was caused by old sessions (a session is a record of the state of the
database after a set up updates has been made) not being deleted correctly
from the database.

To see the benefit from this fix you will need to rebuild the database.

CDS start/end positions

Perhaps not a bug, more a confusion in meaning. For a sequence object that
is a CDS you can specify the start/end positions of the CDS within the
accompanying Source_exons and here in lies the problem. The start/end
positions must be specified in spliced DNA coordinates, _not_ in Source_exon
coordinates. This means you have to do some mental arithmetic if you are
inserting the CDS positions by hand: you will need to add up the length of
the Source_exon sections to get the size of the spliced DNA and work out
where the CDS starts and ends within the single continuous section of exon

acedb will now output an error message if a CDS is displayed where the
start/end positions lie outside of the spliced DNA and will display the CDS
as if it occupied the entire length of the spliced DNA.

CDS start/end positions not working for reverse genes

There was an annoying bug whereby, for reverese genes only, acedb would
ignore a CDS start position unless an end position was specified as well.
This has been fixed so that a CDS for a reverse gene now behaves the same
way as for forward genes.

Obscure socket server bug

When started by inetd, the socket server crashed inetd on some linux systems
because it wrongly _"shutdown"_ the listening socket when exitting. This has
been fixed.

XREF problem

There has been a bug in the XREF code when making updates to a database for
a long time. In 4_8 this has manifested itself in the form of updates
failing where they involve XREFs with UNIQUE tags. This seems now to be
fixed at long last, if this is not so then please send reports to
acedb at sanger.ac.uk.

This is an important bug to fix because it has been the principal reason for
not releasing updates to large databases as "diffs". Currently databases
such as the Worm database have to be released as complete new copies every
time there is an update. Now the Xref bug is fixed it should be possible to
release an update file which consists only of those parts of the database
are different since the previous relase.

No monthly build available.

Unfortunately, due to system problems at the Sanger Centre a monthly build
has not been possible for September.

Next User Group Meeting - D213, 2.30pm, Thursday, 14th September

Ed Griffiths <edgrif at sanger.ac.uk>
Last modified: Thu Nov 30 15:30:54 GMT 2000

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