[Genex-users] Re: [GeneX-dev] fix-array.pl script error

[<ja...@op...>]

Hrishikesh Deshmukh <gen...@ya...> writes:

> Where do i find these scripts?!

Hey Hrishi,

(I've Cc:ed the genex-users list since this is probably the best place
to archive the discussion)

These files all live in the genex_server distribution in the
DB/curated_data/ directory.

Cheers,
jas.

> Hrishi
>
> "Jason E. Stewart" <ja...@op...> wrote:
> Hrishikesh Deshmukh writes:
>
>> Yes in deed thats the last line in the file but what does it mean
>> and how do i fix it!
>
> Hey Hrishi,
>
> Did this happen after we talked? If so, this is what I meant by
> needing to rewrite fix-array.pl for each type of input file. It is set
> up to only handle quantarray data files for input. You'll notice there
> are 5 different scripts:
>
> * fix-array-cel.pl - .cel file input
> * fix-array-mas4.pl - mas4 input
> * fix-array-mas5.pl - mas5 input
> * fix-array.pl - quantarray input
> * fix-array-qa.pl - yet another version of quantarray input
>
> You should probably look at the other ones, they are most recent - the
> original fix-array.pl was for mangling the probe names in one of
> Karen's original data files.
>
> There are two ways to fix this:
> 1) put a sample input file on genex2 and tell me where to find it so I
> can write a script to handle it
> 2) read the comments in the script to understand what the program
> does, and modify it to work with your input.
>
> This are very simple scripts. All it does is go through every line of
> the input file and writes out a simplified version that only has the
> necessary pieces. The script needs to know:
> 1) when to start reading in the spot data (that's what the two perl
> regular expressions $data_start_regexp and $reading_data_regexp are
> for
> 2) what data columns to keep in the output file
> 3) how to create a unique spot_identifier for each row of data. Affy
> files have a unique probe name, quantarry files use a concatenation
> of the four values: row, column, grid_row, and grid_column.
>
> Requiring ArrayDesign's is a *painful* part of data loading - but this
> is something that only curators should ever have to do. It is needed
> by the system because we have to map every expression value in the
> data table to a spot on a chip - and to do that we need a uniform way
> of creating spot_identifiers.
>
> If someone comes up with a better approach I will be forever grateful.
>
> Cheers,
> jas.
>
>> Harry Mangalam wrote:
>> Hi Hrishi,
>>
>> That's a strange place for genex to be installed - I don't remember installing 
>> it at root, tho I may be mistaken.
>>
>> Also, it's an odd error - there is no '==' at line 230 - I'm assuming it's the 
>> one that finished the stanza at 232.
>>
>> I think this implies that the input is at line 3195 - is that the end of the 
>> file or does that line look peculiar in any way relative to the rest of the file?
>>
>>
>>
>> Hrishikesh Deshmukh wrote:
>>> Hi All,
>>> 
>>> Here is the error which i get when i try to run fix-array.pl script on a 
>>> cDNA file.
>>> 
>>> $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt
>>> Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl 
>>> line 230, line 3195.
>>> Finished
>>> Thanks,
>>> Hrishi
>>> 
>>> ------------------------------------------------------------------------
>>> Do you Yahoo!?
>>> Yahoo! Mail Address AutoComplete 
>>> 
>>> - You start. We finish.
>>
>> -- 
>> Cheers, Harry
>> Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta...
>> <
>>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
>> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
>> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
>> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
>> _______________________________________________
>> Genex-dev mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/genex-dev
>>
>> __________________________________________________
>> Do You Yahoo!?
>> Tired of spam? Yahoo! Mail has the best spam protection around 
>> http://mail.yahoo.com 
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev
>
> 		
> ---------------------------------
> Do you Yahoo!?
> Yahoo! Mail - 50x more storage than other providers!