[BioC] CLF/PGF parser

[James W. MacDonald]

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?

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.