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: [email protected] 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 [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
