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Full Discussion: awk to count and rename based on fields
Top Forums Shell Programming and Scripting awk to count and rename based on fields Post 302980380 by cmccabe on Friday 26th of August 2016 01:23:07 PM
Old 08-26-2016
awk to count and rename based on fields
In the below awk using the tab-delimited input, I am trying count the - symbol in $5 and output the count as well as the renamed condition ins. I am also count the - symbol in $6 and output the count as well as the renamed condition del. I am also count the tomes that in $5 and $6 there are actually letters in both, and output the count as well as the renamed condition snp.

input
Code:
Index    Mutation Call    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    Sanger
13    c.[1035-3T>C]+[1035-3T>C]    166170127    166170127    T    C    intronic    SCN2A        
16    c.[2994C>T]+[=]    166210776    166210776    C    T    exonic    SCN2A    synonymous SNV    
19    c.[4914T>A]+[4914T>A]    166245230    166245230    T    A    exonic    SCN2A    synonymous SNV    
20    c.[5109C>T]+[=]    166245425    166245425    C    T    exonic    SCN2A    synonymous SNV    
21    c.[5139C>T]+[=]    166848646    166848646    G    A    exonic    SCN1A    synonymous SNV    
22    c.3152_3153insAACCACT    166892841    166892841    -    AGTGGTT    exonic    SCN1A    frameshift insertion    TP
23    c.2044-5delT    166898947    166898947    A    -    intronic    SCN1A        
25    c.1530_1531insA    166901684    166901684    -    T    exonic    SCN1A    frameshift insertion    FP

current output
Code:
Category  Count
ins       del    2

desired output
Code:
Category  Count
ins           2
del           1
snp           5

Last edited by cmccabe; 08-26-2016 at 02:23 PM.. Reason: fixed format
 

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LEARN ABOUT CENTOS

clags2

clags2.f(3)							      LAPACK							       clags2.f(3)

NAME

       clags2.f -

SYNOPSIS

   Functions/Subroutines
       subroutine clags2 (UPPER, A1, A2, A3, B1, B2, B3, CSU, SNU, CSV, SNV, CSQ, SNQ)
	   CLAGS2

Function/Subroutine Documentation
   subroutine clags2 (logicalUPPER, realA1, complexA2, realA3, realB1, complexB2, realB3, realCSU, complexSNU, realCSV, complexSNV, realCSQ,
       complexSNQ)
       CLAGS2

       Purpose:

	    CLAGS2 computes 2-by-2 unitary matrices U, V and Q, such
	    that if ( UPPER ) then

		      U**H *A*Q = U**H *( A1 A2 )*Q = ( x  0  )
					( 0  A3 )     ( x  x  )
	    and
		      V**H*B*Q = V**H *( B1 B2 )*Q = ( x  0  )
				       ( 0  B3 )     ( x  x  )

	    or if ( .NOT.UPPER ) then

		      U**H *A*Q = U**H *( A1 0	)*Q = ( x  x  )
					( A2 A3 )     ( 0  x  )
	    and
		      V**H *B*Q = V**H *( B1 0	)*Q = ( x  x  )
					( B2 B3 )     ( 0  x  )
	    where

	      U = (   CSU    SNU ), V = (  CSV	  SNV ),
		  ( -SNU**H  CSU )	( -SNV**H CSV )

	      Q = (   CSQ    SNQ )
		  ( -SNQ**H  CSQ )

	    The rows of the transformed A and B are parallel. Moreover, if the
	    input 2-by-2 matrix A is not zero, then the transformed (1,1) entry
	    of A is not zero. If the input matrices A and B are both not zero,
	    then the transformed (2,2) element of B is not zero, except when the
	    first rows of input A and B are parallel and the second rows are
	    zero.

       Parameters:
	   UPPER

		     UPPER is LOGICAL
		     = .TRUE.: the input matrices A and B are upper triangular.
		     = .FALSE.: the input matrices A and B are lower triangular.

	   A1

		     A1 is REAL

	   A2

		     A2 is COMPLEX

	   A3

		     A3 is REAL
		     On entry, A1, A2 and A3 are elements of the input 2-by-2
		     upper (lower) triangular matrix A.

	   B1

		     B1 is REAL

	   B2

		     B2 is COMPLEX

	   B3

		     B3 is REAL
		     On entry, B1, B2 and B3 are elements of the input 2-by-2
		     upper (lower) triangular matrix B.

	   CSU

		     CSU is REAL

	   SNU

		     SNU is COMPLEX
		     The desired unitary matrix U.

	   CSV

		     CSV is REAL

	   SNV

		     SNV is COMPLEX
		     The desired unitary matrix V.

	   CSQ

		     CSQ is REAL

	   SNQ

		     SNQ is COMPLEX
		     The desired unitary matrix Q.

       Author:
	   Univ. of Tennessee

	   Univ. of California Berkeley

	   Univ. of Colorado Denver

	   NAG Ltd.

       Date:
	   November 2011

       Definition at line 158 of file clags2.f.

Author
       Generated automatically by Doxygen for LAPACK from the source code.

Version 3.4.2							  Tue Sep 25 2012						       clags2.f(3)
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