EMBOSS: Project Meeting (Fri 3rd September 2004)
1. Minutes of the last meeting
Minutes of the meeting of 20th August 2004 are
2. Software Development
Jon has worked through Ranjeeva's applications. They can now
read "any" alignment or sequence format, adapted as simple extensions
of FASTA etc.
Documentation has been updated. New functionality that is not needed
or over-engineered has been stripped, making it easier to document
and use the programs.
Gary has modified diffseq, as requested by Tim, to show SNPs
that change translations. A feature routine has been
contributed. There are a few problems to be resolved with frames
across multi-exon genes. A microbial version will be passed to Tim
for testing at Sanger.
Alan has Jemboss running on AMD64 with at least one version of
Peter has fixed a problem in the old phylip with null
characters appearing in species names. No users had reported this - it
was found by QA testing.
2.5 XML output
Peter reported that EBI external services have an XML format
for tool output which he will consider for EMBOSS output (as outdata
and as sequence, feature, report or align output).
2.6 Split entries
Tim requested a program (possibly entrezsplit) to return split
entries. This would need to split the feature table without losing
feature information - tricky as it involves splitting the sequence,
extracting a subset of the feature table, and copying all other text,
and also is quite specific to EMBL format.
Output file naming would also be complicated, but can follow the
-ossingle model for sequences.
3.1 ACD talk
Peter's postponed ACD update talk will be next Friday (10th).
4.2 User survey
Over 800 replies so far.
4. Documentation & Training
Alan will revise the book chapter outlines..
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
7. Date Of Next Meeting
Next meeting at 9.30 on September 17th, 2004,