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Full Discussion: Awk: get upper and lower bound per group
Top Forums Shell Programming and Scripting Awk: get upper and lower bound per group Post 303007263 by genome on Tuesday 14th of November 2017 04:43:33 PM
Old 11-14-2017
Awk: get upper and lower bound per group
Hi all,

I've data as:
Code:
22      51018157        51018157        exonic  CHKB    nonsynonymous SNV
22      51018204        51018204        exonic  CHKB    nonsynonymous SNV
22      51018428        51018428        exonic  CHKB    nonsynonymous SNV
22      51018814        51018814        exonic  CHKB    nonsynonymous SNV
22      51019001        51019001        exonic  CHKB    nonsynonymous SNV
22      51019849        51019849        exonic  CHKB    nonsynonymous SNV
22      51020736        51020736        exonic  CHKB    nonsynonymous SNV
22      51021027        51021027        exonic  CHKB    nonsynonymous SNV
22      51021197        51021197        exonic  CHKB    nonsynonymous SNV
22      51063758        51063758        exonic  ARSA    nonsynonymous SNV
22      51063778        51063778        exonic  ARSA    nonsynonymous SNV
22      51063820        51063820        exonic  ARSA    nonsynonymous SNV
22      51063845        51063845        exonic  ARSA    nonsynonymous SNV
22      51064416        51064416        exonic  ARSA    nonsynonymous SNV
22      51064489        51064489        exonic  ARSA    nonsynonymous SNV
22      51065266        51065266        exonic  ARSA    nonsynonymous SNV
22      51065287        51065287        exonic  ARSA    nonsynonymous SNV
22      51065341        51065341        exonic  ARSA    nonsynonymous SNV
22      51065361        51065361        exonic  ARSA    nonsynonymous SNV
22      51066194        51066194        exonic  ARSA    nonsynonymous SNV
22      51143462        51143462        exonic  SHANK3  nonsynonymous SNV
22      51153371        51153371        exonic  SHANK3  nonsynonymous SNV
22      51159778        51159778        exonic  SHANK3  nonsynonymous SNV
22      51160154        51160154        exonic  SHANK3  nonsynonymous SNV
22      51169684        51169684        exonic  SHANK3  nonsynonymous SNV
22      51176664        51176664        exonic  ACR     nonsynonymous SNV
22      51176734        51176734        exonic  ACR     nonsynonymous SNV
22      51177812        51177812        exonic  ACR     nonsynonymous SNV
22      51178286        51178286        exonic  ACR     nonsynonymous SNV

It's a tab separated data.
Column one is chromosome
Column two is start position, three is end. Column fifth is gene name.

My desired output is

Code:
22 CHKB 51018157 51021197
22 ARSA 51063758 51066194
22 SHANK3 51143462 51169684
22 ACR 51176664 51178286

That is, for each gene, I get the smallest number from column 2 and largest from column 3.

I could only get my head around this much:
Code:
 cat small_d.txt | awk '{a[$5]=$1} END {for (i in a) {print i,a[i]}}'

I can't simply think in awk. I can write a python script but would like to learn these magic tricks.
Last edited by Scrutinizer; 11-14-2017 at 09:32 PM.. Reason: edited output; mod: changed quote tags to code tags
 

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LEARN ABOUT CENTOS

clags2.f

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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