EMBOSS: Project Meeting (Feb 28th 2000)
system calls still need to be changed, and any rm calls need to be "unlink" instead.
Peter has changed output to stdout and stderr by a few applications to use ajUser, ajFmtprintF to the output file, and in a few cases ajDebug.
HGMP databases need to be added to the documentation pages, and could be added to the example emboss.default template file.
The -acdpretty option should stop the program.
Gary would like an application to extract the full text of a database entry. Peter will modify sequence reading to store all input as text and echo it to a file in a new application "seqdoc", but with no guarantee of correctness. For example, a GCG version of an EMBL entry will have spaces in the feature table's ".." locations.
Peter has a solution to floating point rounding problems in alignment algorithms for large sequences.
Logging is now enables at HGMP. Many users are running infoseq.
A random filename for temporary files would be useful. There is a simple one already in emma.
Some further testing is needed before committing these changes.
An alternative font for alphanumeric characters in graphics output would be useful.
The email return of results needs to change. Results are stored in temporary disk space for up to 5 days.
Some database entry USAs are allowed, for example SWISSPROT:entry_name in needle, but wildcards are not allowed. One option is to add new wildcards to the USA syntax for use in PISE.
PISE now has a startup script (optionally) to setup the user environment for EMBOSS.
For feature locations that are not simple start and end positions, new tag values to hold the location as text would be useful.
It was proposed to first implement an EMBOSS interpretation of GFF output, and then to post this for discussion to the GFF mailing list.
Gary is writing showfeat to display features. There are still some problems with missing feature tables.
Next meeting will be Monday 6th March 2000, 11:00am, usual place.