Hi Richard, Forgot to say after your last mail (ages ago now), thanks for all your help! The stuff I'm using the Nexus parser in works great now.
Cheers, -David 2009/8/11 Richard Holland <[email protected]>: > It should already be on CruiseControl. > > Standards in bioinformatics are a pain - people write them to describe the > format of files their software outputs, then the very same people then > produce files that break those standards without any additional > documentation or explanation. (Genbank are one of the biggest offenders!) It > makes it very hard to write parsers, because if you stick to the official > spec there will always be files that don't work yet people insist are still > valid, yet without prior documented evidence of invalid files that are > considered to be valid, it is impossible to write a parser to cater for > them. :) > > cheers, > Richard > > On 11 Aug 2009, at 11:12, David Johnson wrote: > >> Hi Richard, >> >> OK that's good to know... I suppose that's the problem with specifications >> - people don't always follow them! >> >> But I get the impression either some people think that using >> interleave=yes/no is standard practice, or it could be being generated by >> some other phylo software (e.g. maybe PAUP or some other tools). >> >> I had a talk with my supervisor and he actually can't find the specific >> programs that have been putting that in, but looking at a range of his Nexus >> files, there's quite a few that seem to use put in the yes/no bits, some >> files he received from other researchers. >> >> Are the modifications available in the latest automated build (on >> CruiseControl)? >> >> Cheers, >> -David >> >> 2009/8/11 Richard Holland <[email protected]> >> I've found the problem - "interleave=yes" is not valid according to the >> official NEXUS format spec which the parser was written against. (Maddison >> et al., 1997) >> >> Interleaved file are supposed to only include the word "interleave" - it >> takes no parameters. Non-interleaved files shouldn't mention it at all. >> >> I've modified the parser to tolerate this but I'd be interested to know >> where the invalid token came from - was it added manually, or by an existing >> piece of publically available software? >> >> The modification has been made in the trunk of the biojava-live subversion >> repository. >> >> cheers, >> Richard >> >> _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
