EMBOSS: Project Meeting (Tue 19th May 09)
Peter has updated the PHYLIPNEW code to phylip release 3.68. Mahmut had found a bug in reading large input files which was fixed in this phylip release. Changes to applications derived from seqboot need to be checked, and all applications need to be run through QA tests to check for changed results before committing to CVS.
Peter will add some of these standards to the code documentation parser so that the standards can be maintained more easily.
Alan will clean up the remaining AJAX files (ajseqwrite and ajstr) and clean the NUCLEUS library. It was agreed that application code can remain in its current state as the main issue is library code examples and documentation for the books and website.
Peter has put the distance matrix input format patch on the FTP server. The code in ajphylo.c failed to read some distance matrix files where lines were long enough to be wrapped.
Mahmut identified an issue with SRS as a data access method. If only part of the sequence data was read - for example by nthseq - the call to getz failed to complete. Peter will investigate.
Mahmut has looked into BioPerl parsing of EMBOSS output. A user requested the start and end positions of a local alignment, which was easily resolved. The same user now wants to retrieve the full sequence ID. In the default alignment output, based on FASTA program output, the ID is truncated to 6 characters. Peter will consider changing the format, or introducing a new format for BioPerl to parse. BioPerl is capable of setting the alignment format when launching an application.
Peter and Mahmut attended a meeting on next generation sequencing bioinformatics in Cambridge. The University plans to set up a wiki to discuss the issues raised, and will organise a follow-up meeting towards the end of the year.
Alan has reviewed and updated the Administrator Guide.
Jon has converted the "GCG to EMBOSS conversion" section to XML.
At a meeting with the publishers, it was agreed that the book text would be completed by 24th August (40 days after the 6.1.0 release).
Jon will test conversion of the text to HTML and send a sample chapter to the publishers to test for format and editing issues.
Peter is investigating the current MEGA sequence format which has changed from the version EMBOSS reads and writes. A local installation (free) will be needed to test the current formats read and written by MEGA, which runs on Linux under the WINE windows emulator.
Jon will look into some questions on HMMER posted directly to the sourceforge tracker.
Alan has a question from David Judge about the writing of the one line description to standard error. He is using Artemis, and should put -auto on the command line to disable writing of the description.
Alan reported an issue with the possible complexity for new developers of returning "const char*" pointers to internal strings. The configure option --enable-devwarnings is required to warn of casts to non-const types.