ACEDB User Group Newsletter - July 2002

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Several new features this month including a "-tsuser" option so you can fake who is doing the updates to a database (!), a "nosave" command so you can test scripts without destroying your favourite database, the fixing of numerous bugs and some stuff about the coming of Smap.

General News

We continue to wade through the introduction of SMap into FMap and it continues to produce unexpected bugs but we are getting there.

New Features

New -tsuser command line option

All AceDB programs now accept a -tsuser commandline option of the format:

-tsuser "new_username"

By default the username for a database session is the userid you logged in with. You can use -tsuser to set a different username for the session. This is useful in at least two situations:

1. If you are using various scripts to interface to tace or giface to make updates to the database, you can use the -tsuser option to use the name of the script instead of your login name for the updates, that way you can be sure which updates were made by which scripts.
2. If you have a number of developers who all access the database from the same userid for access permissions reasons, by setting the username for each database user you can keep track of the updates made by the different users.

New "Nosave" command

You can now turn on and off saving by acedb using the "Nosave" command:

NoSave [-stop | -start]
   Stop or start all database saving, the -stop option prevents any saving by any command,
   you must use the -start option to turn saving on again.
      -stop   (default) turn saving off
      -start  turn saving on.

This is particularly useful if you want to test scripts that use tace for large scale database updates without accidentally altering the database during testing. By setting saving off at the start of the script, you can get all your data parsed by acedb so see if its correct but it won't be saved in the database.

New giface "smap" command

SMap has been made available via the giface interface so it's possible to find out the positions of one feature in its parent. The command interface is:

smap -coords x1 x2 -from class:object -to class:object

The command maps the coordinates x1, x2 (default is the whole object) in the "-from object" to coordinates in the "-to object", the former must be a child of the latter via SMap or Sequence tags.

The command returns a string in the following format:

"SMAP  class:name y1 y2 nx1 nx2 status"

Where

• class:name is the class and name of the parent object.
• y1 y2 are the coordinates of the child in the parent object.
• nx1 nx2 are the coordinates in the child that were actually mapped to produce y1 and y2, these will have changed if the original coordinates had to be clipped to fit in the range of the parent object.
• status is an smap status code which indicates whether the mapping was perfect or clipped in some way.

Articles

Removal of Match_Table support

Prior to the introduction of SMap, there was a problem with large numbers of homologies being processed/displayed in the FMap because the homologies had to be embedded in the Sequence objects. The Match_Table tags could be used to specify which homologies were processed/displayed. Few users made use of this tag and since the SMap now allows homologies to be held outside of the sequence objects, support for these tags has been removed from the code (as advertised in the acedb newsgroup some months ago).

Bugs Fixed

Bug in GFF dumper

Code was added to flip the strand of ESTs that were sequenced in reverse so that they were displayed on the correct strand in Fmap. These were not flipped back for GFF dumping, this is now fixed.

Bug in Confirmed Intron code

A bug in the code that allocated segs for confirmed introns sometimes corrupted the parent sequences reference to its seqinfo struct, this caused the genomic canonical column to be incomplete.

Bug in CDS positioning

The CDS positioning code did not handle exons of length 1, now fixed.

Bug in blixem call to pfetch sequence

Code was giving wrong args to pfetch to get just the sequence, now fixed.

Bug in CDS drawing code

Obscure bug, a wrongly initialised variable led to incorrect drawing of the CDS, but only when two sequence objects with same method, on same strand in same position with CDS's were being displayed.

Bugs in Temp Gene

A number of bugs have surfaced in the Temp Gene code caused by changing the code to recalculate after a new gene is made rather than just redraw. This included problems with working out reverse complement coords, initialise() no longer being called in the necessary places, a bug in corrupting the dna array surfaced, a bug in fMapFindSpan() and so on. All fixed now.

Developers Corner

This month has seen a lot of bugs discovered and fixed which come down to problems with interactions between SMap and FMap and also the problems of introducing "recalculates" into parts of FMap where their used to be redraws which has revealed that FMap contains quite a lot of state that goes stale when this happens and produces bugs that are hard to notice and find the cause of.

I include the below simply as pointers to the type of things that have been going on:

• Bug in sMapLength, if there are mixed sMap and ACE4 tags, we should use both.
• Fix up sMapFindSpan so that it knows only about 1-based coords, this is the standard for smap stuff. Make sure that other smap calls used sMapFindSpan correctly.
• Fix bug in sMapFindSpan(), meant that it would never find the span for the given coords.
• clear look->chosen hash on recalculate - it contains stale data.
• fix setStartstop to cope with 1,0 coords - as when called in giface
• Fix code that does coords for recalculate, it was broken because we don't use fmapFindDNA any more which used to frig the coords. The new rules are encapsulated in setStartStop().
• Add code to fMapDoRecalculate() to make sure that any new start/stop include current active zone, this became a problem with smap code because we get hold of the sequence a bit differently, but was also a problem as far back as 4_7 if you scrolled in just the right way.
• Fix up setTempGene() so that it works out reverse complement coords correctly because we now use keys, not segs, to do coords stuff.
• Fix bad bug which sometimes corrupted the dna array by inserting a C "end of string" char but then not removing it.
• initialise() was not called from all the places it should have been, this did not matter previously because bsUpdate() and other operations were done on _VSequence, now a static holds the class, if the static is not initialised the code eventually crashes because the key does not have the correct class for the bsNNN calls.
• fMapFindSpan() is now really a call to sMapFindSpan() but this is all messed up because of confusion over coordinate systems: smap stuff should ALL BE ONE BASED. Otherwise you get bugs like the one in fmapgene where everything is suddenly off by one.
• fix bug in seg flipping for complementing when something is clipped by smap, need to reverse which end is clipped.

July monthly build not available.

Apologies, once again there was no build this month due to the major SMap development work.