EMBOSS: Project Meeting (Mar 23rd 2000)


Sanger Centre: Peter Rice, Ian Longden
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Jon Ison

1. Matters Arising

The meeting was postponed from March 13th due to the unavailability of some people and a clash with Sanger internal courses.

2. General progress on release 0.0.4

Peter used Val's HGMP tutorial for the Sanger course earlier this week. It was very well received by the students.

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.

3. Graphics

Xwindows displays at HGMP are giving serious problems, with black graphics windows appearing. One possibility is a clash with applications such at Netscape running at the same time. Peter and Ian will investigate. The problem has so far not been reported by any other site.

4. Interfaces

The Trends reviewers commented that there are no links back to EMBOSS from the main interface sites we are aiming to work with. To work around this, Peter will work on web pages for the EMBOSS site describing the other interfaces and how EMBOSS can (or does) integrate with them.

5. Features

Ian has implemented EMBL and GFF feature dictionaries. The EMBL dictionary is taken from the EBI's feature table definition. The GFF dictionary includes a few common additions to the EMBL features. The files are in the EMBOSS data directory: features.embl and features.gff for the feature keys (EMBL) or names and tags (GFF) plus tags.embl and tags.gff for the feature qualifiers/tags and value types.

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.

6. Any Other Business

The Trends in Genetics article has been revised and resubmitted. The more technical detail has been reduced, and a general overview of key applications and example interfaces has been added.

7. Next meeting

Meeting on Monday 10th April, 11:00am, usual place.