EMBOSS: Project Meeting (May 15th 2000)
Peter is working on modifications to output file and sequence range types in ACD.
Using the "-ossingle" qualifier, or implying it with GCG format output, should not create an output file in ACD processing as it is ignored later.
Gary updated fuzztran output formatting.
Peter has completed coding sequence database reading for BLAST formats. This will need further testing next week before being committed. All blast formats are covered (NCBI 1 and 2, DNA and protein, with optional FASTA file to resolve DNA ambiguities) with the exception of the new BLAST 2 multi file format where there are currently no examples at Sanger. However, the EMBOSS EMBLCD/Staden index file format will cope with multiple files and so this can be easily extended.
The ajSeqMakeUsa function has some problems still, for example db:* names, and some list files. Peter will investigate.
Peter is looking into phylogenetics and sequence alignment formats for an alignment database project at EBI. Output is available, and was easy to do. Examples of the formats are needed to make sequence reading work robustly.
Alan has implemented dynamic arrays as AjPInt, AjPInt2d, AjPInt3d (etc.) for integer, long, short, float, and double, with up to 3 dimensions each.
We should aim for a beta 1.0 release as soon as possible. Probably when the documentation updates and sequence reading are in place.
Links to the EMBASSY applications are not correct on the web pages. Also, EMBASSY applications are not included in the group pages. Peter will investigate.
Val proposed parent and child groups for applications. Gary will change wossname and Peter will look at documentation and library changes.
Peter is writing a web page on the various interface collaborations.
The Sanger documentation pages need to change to be usable at HGMP and to be distributed to other sites. Peter will work on a simplified version without the stylesheets and sidebar.
The ChangeLog file does not include much information on code changes (actually, it is still empty). Peter will make a merged file CvsLog from the CVS logs at Sanger and HGMP.
Next meeting on Monday 22nd May, 11:00am, usual place.