EMBOSS: Project Meeting (Feb 7th 2000)

Attendees

1. Matters Arising

2. General progress on release 0.0.4

The graphics options for pepinfo need to be changed to use the standard graph types. The current options were a workaround for problems with the ajhist library. Ian and Mark will look into this.

PISE has problems with HTML tags in some output. Peter will remove them.

The "entrails" program to show the internal data definitions should report:

• sequence formats
• database definition options (actual definitions are reported by showdb)
• standard data files (embossdata reports all files but there is no easy way to check every possible local data files for matrix, codon and other types.

Peter is working on conversion of ACD files to XML and on XML output format(s). He will check with Catherine Letondal on the current requirements for PISE.

infoseq uses tabs as an output delimiter. Spaces would be cleaner, before automated scripts begin to depend on the tabs (as happened with GFF feature format).

HGMP user feedback has been positive. Logging would be useful. Peter will add this, with a simple log of application, useranme and date/time. By default, logging will be turned off.

HGMP have most databases indexed. Peter will remove the warnings for excluded data files now that they seem to be working, and replace them with ajDebug calls.

Documentation is the main requirement for a first release. Peter will continue to work through the application files.

Sequence features should be implemented as the major enhancement for release 2.0, which simply means not turning features on until they are fully implemented though work can start now. Ian, Richard and Peter will work on this.

4. Any Other Business

Amy Williams (Leeds) will work on analysis of silent mutations.

David Martin will have someone to work on graphics extensions.

5. Next meeting

Next meeting will be Monday 14th February 2000, 11:00am, usual place.