aipl2uga.sh

Olivier Filangi, 16/05/2012 14:40

Télécharger (397 octets)

 
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#!/bin/bash
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# this script changes a SNP file (arg1 on entry) from AIPL to UGA format and generates the cross ID file
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# new file will be $1_UGA
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echo `wc -l $1 | awk '{print $1}'` "lines in" $1
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#


    		
  

  

    
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awk ' {nsnp=length($3);


    		
  

  

    
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	printf("%10s%1s%" nsnp "s\n",$1," ",$3)}' $1 >$1"_UGA"


    		
  

  

    
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echo `wc -l $1"_UGA" | awk '{print $1}'` "lines in" $1"_UGA" 


    		
  

  

    
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awk '{print $1,$1}' $1"_UGA" > $1"_UGA_XrefID"


    		
  

  

    
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