EMBOSS: Project Meeting (Jan 17th 2000)


Sanger Centre: Peter Rice, Ian Longden
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Sinead O'Leary

1. Matters Arising

2. General progress on release 0.0.4

Peter has added -goutfile for graph objects so they now match xygraph, expect that the data output type is not allowed as it only makes sense for the xygraph type.

Val will install and test PISE. An ACD textwidth field would be useful to provide wider boxes for text input.

supermatcher has a bug. Peter and Ian will investigate.

Peter will try to find simple examples for most applications and add them to the documentation. The help output and the table of command line options are now generated automatically each night.

Peter has added an array data type to ACD, which is floating point (AjPArrayf) for use by PHYLIP applications. Arrays can be set to have a set number (e.g. 4) items, and a set total (e.g. 1.0) with a tolerance which is the absolute difference between the true and expected total. This defaults to 0.01.

Peter is working on sequence database subsets

Peter will look into adding a "Set of sets" sequence type, provisionally names "SOS", when updating sequence reading for the database subsets.

Ian has modified the MSE editor to use the ACGT keys for nucleotide sequence entry.

Alan has noted a bug in the DBI indexing programs in failing to check the return codes from some file operations. Peter will investigate.

A USA function is still required.

Ian is working on porting TOPO, from Susan Johns, to display transmembrane proteins given a prediction of where the transmembrane regions are.

Gary has completed nthseq, a utility to return one sequence from a large input set.

The EBI have offered to support an EBi Industry Programme workshop on EMBOSS in August. There will be funding for external speakers.

Peter van Heusden would like to index FASTA format files with dbiflat. Peter will add a parser for FASTA headers.

3. Any Other Business

4. Next meeting

Next meeting will be Monday 24th January 2000, 11:00am, usual place.