EMBOSS: Project Meeting (Mon 28th March 11)
Minutes of the meeting of 14th March 2011 are here.
Alan has updated primer3 to report the primer length.
Jon suggested reviewing the EMBASSY packages and updating them for the release. HMMER 3.0 is an obvious example. The interface appears similar to the latest HMMER2 wrapping, though the internals are very different.
Peter noted that ViennaRNA has been updated. Other packages should also be checked for more recent versions.
Jon noted that the next Clustal release may need a rewrite of emma or a new EMBASSY package if the interface has significantly changed.
Peter is implementing multi-location features (e.g. joins in EMBL) as sub-features. This will simplify feature sorting, and the reporting of hierarchical feature outputs such as DAS. By removing he need for the CHILD flag, we may be able to avoid using the feature flags special tag in the great majority of practical cases. Peter will test for compliance with the GFF3 features format. EMBOSS uses the same syntax as GFF2 for tag values. These should be unquoted, with commas (sadly) and some other values escaped. Only a few extra functions are needed. GFF3 also uses specially named tags Parent, etc. (each with an upper case first letter). These will be implemented as a separate set of tags in the feature object as storing them as 'note="*Parent..."' is complicated by the case-sensitive naming. We may use this syntax to preserve them in EMBL/GenBank format.
Peter suggested implementing a mEMBOSS version of the QA tests. This should be only for development, and will require a Windows Perl installation and modifications to the qatest.pl script to handle Windows directory paths in configuration, commands, and testing output file contents.
Alan is considering adding pkg.m4 to the m4 macro directory to test for the pkg_config utility. This macro file has been stable for some years. Although this will cope with standard systems, there will be possibilities for modified systems to have problems installing EMBOSS and pkg_config in different locations. This is needed for axis2c at present but may soon have more general uses.
Michael suggested making EMBOSS applications into a callable library. Peter will investigate. The coding effort is not large as this would be an interface that calls the application. The effort would be in providing an interface to the application options before launching with the command line built, or options provided in some other (new) form.
A new attribute cachedirectory has been added to the server attributes in ajnam and to the ajNamServerDetails function.
The cache directory could be in a standard location (for example a server-name subdirectory of the user's .embossdata directory) or an environment variable could be used. This is yet to be decided.
Michael us using ajNam calls to read server and database attributes and is generating the server cache file automatically in a showensembl test application without needing cache directories.
Michael suggested checking for Etags values in HTTP headers to find server or data version numbers. This is available for Ensembl but the values are not provided by BioMart. Alan will ask whether the BioMart team will implement them.
Michael noted that the BioMart at OCRI will be updated soon. Alan is expecting a future switch from tab-separated to XML files and has a message in the code to notify when the tab-separated option disappears.
Peter plans to make similar changes to EMBOSS libraries to support circular sequences. There has been no user demand so this was a low priority. The EMBL feature table uses joins for these cases, but a syntax allowing the Ensembl style would be easy to implement
Michael will soon start the addition of ensembl 61 features which should be relatively straightforward.
One user has asked whether EMBOSS could be split into multiple distributions by application domain. This was rejected as it would most probably result in many partial installation. We could in principle make binary distributions of a limited set of individual applications.
BOSC, Bio-Ontologies and ISMB/ECCB in Vienna will be major events this year. Peter and Jon will be attending.