EMBOSS: Project Meeting (Mar 23rd 2000)
As training courses start up, we need better documentation of possibly critical changes to the way programs operate. These should initially go into the CHANGELOG file, and be posted to the emboss mailing list.
Application groups are not clearly defined. Several groups (e.g. Alignment) do not contain all the obvious programs, and some other groups could be merged. Val offered to look through the groups and make the necessary ACD file changes. The web pages will update automatically.
A documentation directory is still needed for the web pages and for the tutorial.
Peter has worked through most of the applications web pages, adding examples of running programs and of output files.
Needle still appears to have a rounding error problem.
Dottup and dotmatcher have problems with axis scales when the two sequences are different lengths. Dotmatcher also swaps the x and y axes.
Alan is working on modifications to restrict.
Peter has updated transeq for a problem with sequence ranges where the sequence begin position from the command line (if used) was being adjusted for twice.
Some programs have optional output files. At present they are always created. An ACD attribute could be added to open them only if needed, though this could be tricky for interfaces which may pick up old output files with the same name.
Gary has added showfeat to display selected features.
Alan has added freak to plot the frequencies of sequence patterns over a sliding window.
A function to return the USA for a sequence is needed urgently. Peter will work on it, at least for the most common cases.
Gary has proposed colourmap settings on the emboss-dev list. They could be stored in a local data file.
Peter proposed adding a list of matrices and codon usage tables to the emboss.defaults file for use in prompting the user with the most common options. It would be too complicated to search through the entire emboss data directory path looking at every file to find all possibilities.
The Sanger Centre CVS server has been reinstalled to allow remote users to use "cvs update" to maintain a local copy of the full distribution.
A flag is set to warn and skip unknown features and tags.
If there are no dictionaries, the code builds its own dictionary from the input.
acedb features are not yet implemented.
Output is in a defined case, but input can accept any case.
Feature input or output is turned on with "feat: Y" in the ACD sequence definition.
Meeting on Monday 10th April, 11:00am, usual place.