EMBOSS: Project Meeting (Mon 14th September 09)
Peter has modified mse for a former GCG user who wants key-based commands as used in the GCG "seqed" editor. Mse had additional functions as a multiple alignment editor so some of these are hard to define as keys have been already allocated. A proposed solution had been sent to the user for testing.
Peter noted that there is a new release of Phylip (3.69). Peter will apply the changes to the EMBOSS version.
Peter will investigate a report of problems with SwissProt output format (note after the meeting - all fixed in the current release).
Peter is working through a few remaining ajGraph function names.
Peter noted that one bug identified in the mse testing was that optional sequence inputs do not work properly. It appears that mse is the only application with an optional sequence input at present. The ACD processing has been changed to define a value for $acdprotein and other attributes of the missing sequence data.
A phylipnew user has been finding problems with distance matrix files containing '-1.000' where a value could not be calculated. These will be readable with a warning, and treated as missing values. Peter will check with Joe Felsenstein to see what we should do to handle these files correctly. It may depend on the application being used.
Peter noted that the "see also" section in documentation could be improved. For example, needle only reports global alignment applications. This could be extended to show other alignment applications by navigating the groups hierarchy.
Some care is needed to check that lists of strings are correctly managed.
Inclusion in EMBOSS raises the issue of adding foreign code and dependencies to the libraries. Alan will try building the code as a separate library, in a directory below ajax. If successful, other candidate code to split out includes ajgraph and ajhist (already built separately), the pcre imported code, and future interfaces to BioMart. We could also split out ajacd as this is usually where the dependencies arise.
Michael Schuster has a few test applications that we can use to try the code.
Jon has updated ACD files for EMBOSS and EMBASSY with relations describing the application functions. The knowntypes.standard file is reformatted to include an EDAM term description for each known type. These need to be added as "relations" attributes for each input and output data type in the ACD files. About 100 new EDAM terms have been added to cover the fine-grain detail.
Peter will analyse the ACD files to check which known types are most used, and which are redundant.
The workstation order is (we hope) now being manufactured. There was a delay in availability of the monitors, and nobody had contacted us to ask about possible substitutes.
SATA disk cables, spare mice and a replacement external backup drive have been ordered.
Peter reported on last week's BBSRC meeting.