[Bioperl-l] correction to docs for Bio::SearchIO::axt

Chris Fields cjfields at uiuc.edu
Sat Sep 16 13:24:51 EDT 2006


Added it.  Anything else?

Chris

On Sep 16, 2006, at 11:43 AM, Cathy Riemer wrote:

> Chris and Jason,
>
> Thanks for taking care of this.  One small suggestion: to add the
> word "many" before "precomputed", since some sites might provide
> LAV (or other formats).
>
> -Cathy
>
>
> On Sat, Sep 16, 2006 at 08:55:27AM -0500, Chris Fields wrote:
>> Jason, Cathy,
>>
>> I changed the POD description to the following in CVS:
>>
>> ....
>>
>> =head1 DESCRIPTION
>>
>> This is a parser and event-generator for AXT format reports.  BLASTZ
>> reports (Schwartz et al,(2003) Genome Research, 13:103-107) are  
>> normally
>> in LAV format but are commonly post-processed to AXT format;  
>> precomputed
>> BLASTZ reports, such as those found in the UCSC Genome
>> Browser, are in AXT format.   This parser will also parse any
>> AXT format produced from any lav report and directly out of BLAT.
>> ...
>>
>>
>> Chris
>>
>> On Sep 16, 2006, at 12:21 AM, Jason Stajich wrote:
>>
>>> right - I guess I meant the only way to get BLASTZ into our  
>>> system is
>>> lav -> axt.
>>>
>>> I will see if someone wants to update the module synopsis to clarify
>>> this point for users or I will get to it when I have time.
>>>
>>> On Sep 15, 2006, at 11:18 PM, Cathy Riemer wrote:
>>>
>>>> Hello Jason,
>>>>
>>>> I noticed an error in the documentation page for the
>>>> Bio::SearchIO::axt parser at
>>>> <http://search.cpan.org/~birney/bioperl/Bio/SearchIO/axt.pm>.
>>>>
>>>> The page states that "AXT format reports [are] typically produced
>>>> by BLASTZ", but actually BLASTZ produces lav output, not axt.
>>>> Sites that provide pre-computed BLASTZ alignments in axt format
>>>> (such as UCSC's Genome Browser) convert them from lav to axt in
>>>> a post-processing step.
>>>>
>>>> -Cathy
>>>>
>>>> ---
>>>> Cathy Riemer
>>>> Center for Comparative Genomics and Bioinformatics
>>>> Penn State University
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list