EMBOSS: Project Meeting (Nov 22nd 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Mark Faller, Val Curwen

1. Matters Arising


2. General progress on release 0.0.4

Ian has ported MSE. The license conditions are up to Will Gilbert. It will be a separate application (EMBASSADIR). Sequence entry still uses keys "QWER" on the top row of the keyboard, which means cut and paste fails. To pick up the new embassy directory and MSE, use "cvs update -d"

Ian has split ajgraph so applications now link to libajax or libajaxg depending on whether they use graphics.

Peter will clean up the ACD internals so that direct references to sequence objects are replaced by constructor and other function calls. This will provide most of the additional functions Ewan Birney needs to use the EMBOSS libraries.

The Sanger anonymous CVS server is now in use by several developers. Some had problems with versions of make and libtool. Ian has updated the README file to explain the issues. Apple powerbook MachTen has a problem with its sed implementation. There is a workaround of deleting one line for these users.

Peter fixed two bugs caused by passing AjPStr to a function and then overwriting the string and reassigning the pointer. Peter will look into using "const" to fix these cases, though it will always be possible to leave out the "const" in a new function. Purify caught the problem.

Peter will look into demonstration applications for feature table output.

Some users are interested in URLs as valid USAs. These will need special handling, just as the "ASIS" format, so that HTTP is recognized.

Alan has a VMS account to test David Mathog's build problems.

The EMBOSS tutorial from the CCP11 "Getting the Most From Your Sequence" course should be added to the EMBOSS Web pages.

Peter has updated the EMBOSS Web pages with a temporary URL. The new Sanger Software Web pages had left margin menus and an alternative header style. One major advantage is that EMBOSS will be easier to reach from the Sanegr top page. The new pages go live later this week.

Peter has updated the application documentation with help built automatically from acdc "appname" -help -noverbose and would like to add a table to document all the command line options. An example is built into antigenic. Comments would be appreciated. The aim is to add the missing detail to the ACD file where possible.

Gary has added "textsearch" to search sequence descriptions.

Ian has added "prettyplotter", a versin of "prettyplot" that should make fewer pen changes on a pen plotter.

Richard is happy to merge "infoseq" and "seqinfo" which have similar functions. "geecee" can also be retured as "isochore" covers the same functions.

Ian has updated the HPGL driver in PLPLOT to fix pen colours.

Peter has code to index and read GCG and BLAST databases, and will implement this by the end of the week.

There is a problem with reading lists of USAs. Val will send Peter an example.

3. Interfaces

Peter is reworking the ACD command line code to cover cases where parameters are specified out of their natural order (for example, an output file specified as a qualifier at the start of the command). Some options could not be specified before, for example output sequence formats "-osformat" for sequences that were not parameters. The solution is to implement the "-osformat_qualifier" syntax discussed a few months ago. This needs some changes to the logic and will be checked in after further testing. The ACD documentation will need updating to cover this and the "-noverbose" qualifier for the help includes. Peter will do this when changes to ACD are implemented.

Jon Ison is in contact with Catherine Letondal about Pise.

Richard Bruskiewich would like to add a module to ACEDB to run EMBOSS applications using ACD to create a user dialogue.

Peter has discussed the aceclient/aceserver code with Jean Thierry-Mieg. The new implementation is sockets based and should be mush easier to use for reading sequences from ACEDB servers.

Peter has examples of www2gcg interface code from Marc Colet. The first aim is to write and convert ACD files for the application she has already, then to use the same methods to interface EMBOSS using ACD files.

Mark has a parser for ACD to DisGUIse which will use "-acdpretty" output to simplify parsing. The same trick could be useful for other parsers.

4. Any Other Business

5. Next meeting

Next meeting Monday 29th November, 11:00am, usual place.