🚀 go-pugleaf

All,

Please find below the July newsletter.

Some people have said they would rather have the newsletter as a text
attachment, send me an email if strongly agree/disagree.....

cheers Ed
-- 
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| Ed Griffiths, Acedb development, Informatics Group,                    |
|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif@sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
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ACEDB User Group Newsletter - July 2003

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@sanger.ac.uk.

-----------------------------------------------

This month sees a new "subset" command, tag counts displayed in the tree
window, a unfortunate delay to cut/paste in acedb text windows, more work on
the Genetic_code class, a question about acedb case sensitivity and object
renaming, future plans for a "son of FMap".

-----------------------------------------------

New Features

Blixem and selected homologies

When you select a homology in the top, "big picture", window of blixem, the
list of homologies below now gets scrolled to the selected homologies.

New "subset" command in tace/giface

(This article is courtesy of Jean Thierry-Mieg who added this new feature
mieg@ray.nlm.nih.gov)

There is a new subset command available from the command line in tace or
giface:

subset x nx : returns the subset of the alphabetic active keyset from x >= 1 of
length nx

This is an extremely efficient way to export long lists or tables to the web
by pieces. You make an active keyset by some query, subset it, make a table
out of the subset and export the table. This is better than making a slice
of a table because this way you only compute the table slice you are really
interested in.

New "Toggle TagCount" menu option in tree display

(This article is courtesy of Jean Thierry-Mieg who added this new feature
mieg@ray.nlm.nih.gov)

There is a new option in the menu of the xace tree display called "Toggle
TagCount". Select it, and you see in green after each tag how many objects
of the same class contain this tag. What is even more interesting is to
activate this option while displaying the models. In that case, you will see
in red all the tags which are not used at all in your database and which you
may wish to remove from your schema.

The counting relies on the internal acedb indexing which was introduced a
few years ago and should be quasi instantaneous.

To see the models, double click them from the main window or select them
from the 'other class...' button of the main window, or type 'find model' in
a query box.

Tag count is disabled in update mode or in show-time-stamps mode.

-----------------------------------------------

Articles

Cut, Paste and Text windows

(This article is courtesy of Rob Clack who has been working on this new
feature rnc@sanger.ac.uk)

The Pfetch window accessible from fmap and the text editor window accessible
from the Update Tree view have both been reverted to the way they were in
release 4_9q, ie before we started fiddling with them.

The attempt to provide copy-and-paste functionality was doomed as long as we
were using GTK 1.2.10 as there is a bug in that release which breaks popup
menus.

This bug is fixed in GTK 2.2.2 but the upgrade to the new GTK is non-trivial
as there are numerous incompatibilities which will need to be addressed.

We plan to do the upgrade later this year, but in the meantime the
enhancements to the pfetch and text editor windows have been shelved.

This means that anyone who has continued to use older versions of Acedb
because of inadequacies in the pfetch and text editor windows can safely
upgrade to the new monthly version.

Genetic_code class: one more time

(Thanks to Jean Thierry-Mieg mieg@ray.nlm.nih.gov who did the original
coding for this feature.)

A previous article described a new class which allows you to specify
different genetic codes for translating DNA to peptides. The proposed model
for the Genetic_code class to do this was:

?Genetic_code   Other_name ?Text
                Translation  UNIQUE     Text
                Start  UNIQUE   Text
                Base1 UNIQUE    Text
                Base2 UNIQUE    Text
                Base3 UNIQUE    Text

The next month this was then revised to include a specific tag for the rare
Selenocysteine amino acid:

?Genetic_code   Other_name ?Text
                Translation UNIQUE Text
                Start UNIQUE Text
                Base1 UNIQUE Text
                Base2 UNIQUE Text
                Base3 UNIQUE Text
                Selenocysteine Remark Text   // Use the Remark to document your
usage of this tag.

After some discussion this has now been revised once more (sorry) because as
far as is known the TGA codon when specifying Selenocysteine also acts as a
stop codon when at the end of a transcript and so can be viewed as an
"alternative stop" in the same was as some codons are alternative start
codons.

Hence it makes sense to have a unified mechanism for both alternative start
and stop codons, the new model for the Genetic_code class looks like this:

?Genetic_code   Other_name ?Text
                Remark Text
                Translation UNIQUE Text
                Start UNIQUE Text
                Stop  UNIQUE Text
                Base1 UNIQUE Text
                Base2 UNIQUE Text
                Base3 UNIQUE Text

An example for Selenocysteine taken from the the Wormbase database
illustrates usage of the Genetic_code class:

Genetic_code : "Selenocysteine"
Translation  "FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG"
Start        "---M----------------------------MMMM---------------M------------"
Stop         "----------**--*-------------------------------------------------"
Base1        "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"
Base2        "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"
Base3        "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"

In this case the TGA codon (in this case in column 15) will specify the
Selenocysteine amino acid (U) instead of its more usual role of being a stop
codon. This happens unless it occurs at the end of a transcript in which
case it specifies a stop, this is indicated by the "*" in the corresponding
column in the data following the "Stop" tag.

Hence alternative Start codons are specified by an "M" in the Start data and
alternative Stop codons are specified by a "*" in the Stop data.

In the case of Worm base the sequence class has been modified to include a
reference to the Genetic_code class in the Origin section:

?Sequence DNA UNIQUE ?DNA UNIQUE Int            // Int is the length
                             .
                             .
          Origin  From_Database UNIQUE ?Database UNIQUE Int     // release
number
                             .
                             .
                  Genetic_code UNIQUE ?Genetic_code

You can see an example of this in Sequence object "C06G3.7".

You should note that when exporting sequences, acedb will not export the
final codon if it translates as a valid stop codon. In FMap however, the
stop codon is displayed so that its possible to see that the transcript ends
correctly.

Case sensitivity and object names

Recently a user sent in the following problem:

     When I was trying to create an instance of an object in ACEDB, I
     encountered some problem. The problem is as follow: I created an
     object called "test" with all lower case. Then I found out that I
     have to use upper case "TEST". Since I realized that ACEDB is case
     insensative, I can't just created a new object called "TEST".
     Therefore, I deleted old object called "test". And then create a
     new object called "TEST". However, somehow, when I fetched the
     object "TEST", I got "test" back even though I have deleted it and
     double checked it several times. It seems that ACEDB has some kind
     of memory system (still remember old deleted object :-)). Can
     someone tell me how to fix this problem? Thank you very much.

This "problem" is in essence caused by the acedb indexing system works and
in particular by the way it handles texts such as the names of objects.
Acedb keeps tables of strings which are indexed in a very efficient way,
entries in these tables are not deleted until the database is rebuilt. Hence
in the above case, when the object "test" is first created an entry is made
in the index for the string "test". When the object is removed the entry
remains in the index, this is done for efficiency otherwise every single
string would require a usage count and object creation, tag usage etc. would
become less efficient. Now when the new object "TEST" is created the name
"TEST" is compared to existing strings in the index in a case insensitive
way and is a match to "test", hence the object is named "test", not "TEST".

This seems contrary until you start to think what would happen when you
update a database. If you wished to update existing objects you would need
to get the case of their names exactly right otherwise your update would
create a new object. In fact the case of all the tags you specified would
also have to be correct and so on and so on. In other words the whole system
is much simpler with case insensitive handling of strings.

So what to do if you wish to simply change the case of an object ?

The answer is to rename the existing object, when you do this the rename
code in acedb will respect the case of the string you wich to change the
object name to. There are a couple of ways to do this:

>From xace:

Choose "Add/Delete/Rename/Alias Objects" from the main acedb window, specify
the name and class of your object and then click on "Rename-Fuse". This will
give you a dialog box where you fill in the new name in the case that you
want.

>From tace:

acedb> parse
-R Sequence oldname newname
ctrl-D

-----------------------------------------------

Bugs Fixed

Database reindex messages

If you were reindexing the database using xace, the messages reporting the
reindexing tended to be lost because they were sent to the terminal from
which xace was started. The messages will now be displayed in popup windows
so you get better feedback that the redindexing has happened.

Blixem not showing homologies correctly (part 25)

Simon Kelley has doggedly nailed a bug in blixem which led to homologies
being incorrectly shown or not shown at all. This bug turned out to be
another case where not all data coordinates were being correctly modified
when an fmap is reverse complemented. This meant that blixem was supplied
with incorrect "gap" array data for the homologies. A tale of real
persistence, well done Simon.

-----------------------------------------------

Future Plans

Configurable error messages

There are several facilities in acedb where it would be useful to configure
the way in which error messages are output and also the way in which the
facility itself runs. A good example of an existing system is the parse
command which will stop at the first failure or the pparse command which
will continue on to the end of the file processing all objects that do not
have errors, discarding ones that do. This gives the user the choice of
whether to stop "on first failure" or not.

Other places where this would be advantageous include: constructing the DNA
for an SMap and constructing a virtual sequence perhaps for FMap display or
GFF dumping.

In particular it would help users if they could select the number of error
messages and also "first failure" when constructing a virtual sequence. In
particular users who have to construct large GFF files from long virtual
sequences could make use of the facility when testing new data in their
databases.

New code is being added to the messaging routines in acedb to provide easier
control of error messaging and when to fail. The new messErrorCond() routine
includes logic to detect the first failure, and whether none, just the first
or all error messages should be output.

This is work in progress as it will require some alterations to the SMap DNA
and SMap convert code.

ZMap, Son of FMap

Simon Kelley <srk@sanger.ac.uk> and myself have been working on a new acedb
display, named "ZMap" for now, which will be a stand alone display acting as
a client that contacts database servers for sequence information. In effect
a client/server version of FMap and acedb.

Simon has been building the new display within xace to test it out and it
will have a number of new features including the ability to split windows
and show different parts of the same sequence.

I have been working on the main scaffold code for the application which will
be multithreaded so that users will be able to cancel or "Stop" display of a
particular sequence in the way that web browsers do and be able to continue
to work on one display while another is being constructed.

The aim is produce a stand alone display incorporating the best parts of
FMap but which can be used against any database that supports the protocol
that the new display uses (likely to be DAS 2 initially).

-----------------------------------------------

Developers Corner

New "chrono" command in tace/giface

(Thanks to Jean Thierry-Mieg who added this new feature
mieg@ray.nlm.nih.gov)

Jean has been revamping the chrono code and has continued this by adding a
"chrono" command to the command line interface:

Chrono {start | stop | show} built in profiler of chrono aware routines

Obviously this only works for routines that have chrono calls built into
them but its a very useful tool for localised profiling.

Change to the way SMap constructs the DNA for a virtual sequence

While constructing some aquila tests for the SMap DNA code I found it hard
to test the mismatch code because SMap didn't work in the way I expected. It
stopped at the first DNA it found in a hierachy.

Small but important change, altered sMapAddDNA() so that it finds all the
dna down a hierachy, not just the first occurrence. This was done because I
was testing dna ambiguity codes and whether we could map objects with both
Source_Exons and DNA and other things.

Adding new tests to aquila

Adding new tests to aquila. We all know we should do it but.....

Well recently I've added a couple of new tests to our overnight aquila runs
to test SMap DNA construction and the new genetic code routines.

Rob (Rob Clack <rnc@sanger.ac.uk>) has been adding to the aquila
documentation to describe how to add tests and its really much easier now
that aquila handles a series of small test script files rather than one huge
file.

If you add a new facility to acedb or fix a difficult bug, try to add a new
test to Aquila.

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July monthly build now available.

You can pick up the monthly builds from:

Sanger users
     ~acedb/RELEASE.DEVELOPMENT
External users
     http://www.acedb.org/Software/Downloads/monthly.shtml

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Next User Group Meeting - D319, 3.00pm, Thursday, 14th August 2003

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Ed Griffiths <edgrif@sanger.ac.uk>
Last modified: Tue Aug 5 10:51:32 BST 2003