[EMBOSS] HTML tag mismatch in acdtable output for fuzzpro

[Scott Markel]

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:  smarkel at 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