EMBOSS: Project Meeting (Sep 20th 1999)
For GFF output, some examples are needed of how ACEDB currently expects to see the tag value fields, together with a list of the agreed vocabulary in the other fields.
Peter has started working on reading sequences from blast 1.4 and blast 2.0 indexed databases, with optional FASTA format files, NCBI index files and if needed EMBOSS index files for rapid ID and accession lookup.
Peter has permission from Bill Pearson to use the code in the FASTA source libraries for reading GCG sequence database .seq files. These will be added to the EMBOSS sequence database access methods. GCG index files will not be used because they are both proprietary and slow. Staden/EMBO-CD style index files will be used instead, with SRS as an alternative indexing method.
Gary is now working on the "showseq" application, which could grow rapidly.
Peter has updated all documentation for library functions in the source code, and this now appears on the HTML pages and un the EFUNC and EDATA SRS databases. There are some source files that are omitted from the index pages for NUCLEUS and AJAX. Peter will update these today.
Many applications still need documentation.
Gary proposed moving the "data" directory up one level. This was agreed, but may need some care if users are updating the current location already.
Alan has looked into linking EMBOSS with the Bioinformatics Template Library (BTL) from Birkbeck College London. BTL is in C++, and EMBOSS fails to compile with a C++ compiler because by emulating C++ we have used some reserved words. The most important are "this" and "bool" which will need to be renamed. Suggestions are welcome!
Hans Ullitz-Moeller (EMBnet Denmark) would like PNG output. PLPLOT may be able to produce PNG in the near future, but we do not have the source code for this yet.
Application "geecee" is no longer needed, and can be dropped from the makefiles.
David Mathog at Caltech is also interested in Windows NT and VMS builds. He will be working on these.
To make Unix installation simpler, and to help with these ports, Ian is writing a true configure script and Makefile.am for PLPLOT. The PLPLOT library will be stored and distributed unpacked so that we can work on changes where needed, and pass them back to the PLPLOT maintainer(s).
Ian recommends a clean checkout with CVS -P to clean up old directories that are no longer needed.
Articles for the CCP11 Newsletter and embnet.news are also planned.
Next meeting Monday 27th September, 11:00am, usual place.