[EMBOSS] HTML tag mismatch in acdtable output for fuzzpro

[Scott Markel]

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:cjfields at illinois.edu] 
Sent: Monday, 05 December 05 2011 6:04 PM
To: Scott Markel
Cc: emboss at 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.
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