Re: [base] raw data files with hyb name in column headings

2008-03-14 Thread Nicklas Nordborg 
Bob MacCallum wrote:
 Hi,
 
 I'm trying to import some ChipSkipper data into BASE2.6.  While configuring
 the raw data importer I see that the files all have different column headings,
 incorporating the hybridisation name e.g. for GS_Flags column:
 
 H_CLQ50 11_control 9/GS_Flags
 H_CLQ50 4_Control 2/GS_Flags
 H_PbICLQ50  7_PbI 5/GS_Flags
 H_PbICLQ50 14_PbI 12/GS_Flags
 
 It looks like I might have two options:
 
 1. preprocess the raw data files with a Perl script to remove the hyb info
from the column headings
 
 2. configure the importer to use column numbers rather than names, e.g. \12\
but I don't know if this works in BASE2.

Yes, it should work.

There is also a third option. You can use regular expressions in the 
column mappings. I think it should be possible to map a column something 
like this:

\.*GS_Flags\


/Nicklas

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Re: [base] raw data files with hyb name in column headings

2008-03-14 Thread Bob MacCallum 

excellent, thanks, will try that.

Nicklas Nordborg writes:
  Bob MacCallum wrote:
   Hi,
   
   I'm trying to import some ChipSkipper data into BASE2.6.  While configuring
   the raw data importer I see that the files all have different column 
   headings,
   incorporating the hybridisation name e.g. for GS_Flags column:
   
   H_CLQ50 11_control 9/GS_Flags
   H_CLQ50 4_Control 2/GS_Flags
   H_PbICLQ50  7_PbI 5/GS_Flags
   H_PbICLQ50 14_PbI 12/GS_Flags
   
   It looks like I might have two options:
   
   1. preprocess the raw data files with a Perl script to remove the hyb info
  from the column headings
   
   2. configure the importer to use column numbers rather than names, e.g. 
   \12\
  but I don't know if this works in BASE2.
  
  Yes, it should work.
  
  There is also a third option. You can use regular expressions in the 
  column mappings. I think it should be possible to map a column something 
  like this:
  
  \.*GS_Flags\
  
  
  /Nicklas
  
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-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]

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