[BioC] CLF/PGF parser

[Kasper Daniel Hansen]

On Jun 14, 2007, at 12:32 PM, James W. MacDonald wrote:

> Hi Kasper,
>
> Kasper Daniel Hansen wrote:
>> Hi Jim (with a cc to BioC so other interested parties can take  
>> note,  and a cc to devnet at affy in case there has been any updates).
>> The strange situation right now is that CLF/PGF files cannot be   
>> parsed using the Fusion SDK (Affy's official file parsing SDK).  
>> There  are codes for parsing the files somewhere inside the source  
>> code of  the EXACT tools (I think - at least somewhere in the  
>> source of one of  Affy's programs). We are however loathe to take  
>> that code and add it  to affxparser because sooner or later, the  
>> SDK ought to start  supporting CLF/PGF files and then the time  
>> spent doing that would be  more or less wasted. Of course that  
>> decision is easier to make when  none of us have a use for parsing  
>> these files at the moment.
>
> In the file format document for the pgf files:
>
> https://www.affymetrix.com/support/developer/fusion/ 
> File_Format_PGF_aptv161.pdf
>
> I find this comment:
>
> Parsing and Writing
> The official C++ parser used by affy can be found in APT under
> sdk/file/TsvFile/PgfFile.h. When possible, parsing and writing of  
> PGF files should
> be done using this code.
>
> I find the same file in the fusion SDK, along with some other files  
> (like DumpPgf.cpp) that look at least like a start. Is this the  
> sort of thing you need, or are you wanting more complete parser?

Well, ahm, it looks like you are better at using grep/find than I am.  
This looks to be it, although a cursory glance at the files seems to  
indicate a different structure than what we are used to. This might  
be because of the use of Tsv stuff.

Anyway, before I humiliate myself further, I should take a closer look.

Thanks, Kasper


> Best,
>
> Jim
>
>
>> I find it somewhat strange that the file format has not been added  
>> to  the official SDK yet (I just checked version 1.09 again and I  
>> could  not find it), and I encourage everyone to mention it to  
>> their  Affymetrix representatives. As soon as that has been done,  
>> we will  start incorporating it into affxparser, something that  
>> should be a  fairly simple task.
>> Kasper
>> On Jun 13, 2007, at 7:49 AM, James MacDonald wrote:
>>> Hi Kasper,
>>>
>>> Do you have any plans to add parsers for CLF/PGF files to  
>>> affxparser?
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>> -- 
>>>
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Affymetrix and cDNA Microarray Core
>>> University of Michigan Cancer Center
>>> 1500 E. Medical Center Drive
>>> 7410 CCGC
>>> Ann Arbor MI 48109
>>> 734-647-5623
>>>
>>>
>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and   
>>> should not be used for urgent or sensitive issues.
>
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and  
> should not be used for urgent or sensitive issues.