Scott, is this something that needs to be addressed on the bioperl end? chris
On Dec 5, 2011, at 7:14 PM, Scott Markel wrote: > We use BioPerl to build EMBOSS command lines in Pipeline Pilot. After > updating BioPerl to 1.6.9 and EMBOSS to 6.4.0 we noticed a problem. There > are HTML tag mismatches that BioPerl, via XML::Twig, can't handle and skips. > In investigating a bit, it looks like there was a change in the acdtable > output. > > Here are EMBOSS command lines for embossversion and acdtable. > >> embossversion > Reports the current EMBOSS version number > 6.4.0.2 > >> acdtable fuzzpro -help -verbose >& fuzzpro_6.4.0.html > > And here are the three sets of tag mismatches in the HTML. All involve an > opening <th> and a closing </td>. > > Lines 66-9: > > <tr bgcolor="#FFFFCC"> > <th align="left" colspan=5>"-sequence" associated seqall qualifiers </td> > </tr> > > Lines 183-6: > > <tr bgcolor="#FFFFCC"> > <th align="left" colspan=5>"-pattern" associated pattern qualifiers </td> > </tr> > > Lines 212-5: > > <tr bgcolor="#FFFFCC"> > <th align="left" colspan=5>"-outfile" associated report qualifiers </td> </tr> > > Scott > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smar...@accelrys.com > Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Secretary, Board of Directors: > International Society for Computational Biology > Chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics > > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss