[EMBOSS] HTML tag mismatch in acdtable output for fuzzpro

[Fields, Christopher J]

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: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.
>> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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>> 
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>> 
>> 
>> 
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> 
> 
>