Yeah, caught Peter's response on that. Just wanted to make sure there isn't anything we need to do from our end :)
chris On Dec 6, 2011, at 2:21 PM, Scott Markel wrote: > Chris, > > I don't think so. We certainly made changes to our BioPerl copy to work > around the EMBOSS bug, but I don't think BioPerl needs to incorporate what we > did (writing a little subroutine to fix the tags). An EMBOSS fix takes care > of our problem. > > Scott > > > -----Original Message----- > From: Fields, Christopher J [mailto:cjfie...@illinois.edu] > Sent: Monday, 05 December 05 2011 6:04 PM > To: Scott Markel > Cc: emboss@lists.open-bio.org; Kristine Briedis > Subject: Re: [EMBOSS] HTML tag mismatch in acdtable output for fuzzpro > > 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