Lookup field in map file Post: 302803917

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Top Forums UNIX for Dummies Questions & Answers Lookup field in map file Post 302803917 by genehersh on Tuesday 7th of May 2013 04:41:14 PM

05-07-2013

Registered User

Lookup field in map file

Hi,

I have two questions which I would massively appreciate help with.

1.

I am trying to insert a field into a file similar to the vlookup function in excel. In column 2 is a gene id for which i would like to insert the full name in the adjacent column. I have a map file (map.file) which has two columns - in column 1 is the gene ID and column 2 is the full gene name

Code:

inputfile.txt
Func	Gene	ExonicFunc	AAChange	Conserved	SegDup	1000g2010nov_ALL	1000g2011may_ALL	1000g2012feb_ALL
exonic	GABRD	synonymous SNV	c.C816T:p.S272S	660;Name=lod=640		0.15	0.34	0.19
exonic	PRKCZ	synonymous SNV	c.T264C:p.D88D	343;Name=lod=33		0.66	0.73	0.63
exonic	PRKCZ	synonymous SNV	c.A318G:p.P106P	389;Name=lod=51		0.21	0.36	0.24

map.file
Gene ID  Full Gene name
GABRD  Gamma-aminobutyric acid receptor subunit delta
PRKCZ    protein kinase c, zeta

desired output

Func	Gene	GeneName ExonicFunc	AAChange	Conserved	SegDup	1000g2010nov_ALL	1000g2011may_ALL	1000g2012feb_ALL
exonic	GABRD  Gamma-aminobutyric acid receptor subunit delta	synonymous SNV	c.C816T:p.S272S	660;Name=lod=640		0.15	0.34	0.19
exonic	PRKCZ protein kinase c, zeta	synonymous SNV	c.T264C:p.D88D	343;Name=lod=33		0.66	0.73	0.63
exonic	PRKCZ protein kinase c, zeta	synonymous SNV	c.A318G:p.P106P	389;Name=lod=51		0.21	0.36	0.24

The second query I have is that i want to be able to filter the file so that the output only contains those fields where for example column 7 <0.5 and column 8 <0.3 and column 9 <0.2 (sometimes there is just a blank in the field which effectively equals 0)

Is there a way to do this so that the filtering is done based on the column header rather than the column number as I have different files which have a different arrangement of columns but with the same headers.

Sorry for the complicated question.

Thanks

genehersh

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clags2

CLAGS2(l)								 )								 CLAGS2(l)

NAME

       CLAGS2  -  compute  2-by-2 unitary matrices U, V and Q, such that if ( UPPER ) then  U'*A*Q = U'*( A1 A2 )*Q = ( x 0 ) ( 0 A3 ) ( x x ) and
       V'*B*Q = V'*( B1 B2 )*Q = ( x 0 ) ( 0 B3 ) ( x x )  or if ( .NOT.UPPER ) then  U'*A*Q = U'*( A1 0 )*Q = ( x x ) ( A2 A3	)  (  0  x  )  and
       V'*B*Q = V'*( B1 0 )*Q = ( x x ) ( B2 B3 ) ( 0 x ) where  U = ( CSU SNU ), V = ( CSV SNV ),

SYNOPSIS

       SUBROUTINE CLAGS2( UPPER, A1, A2, A3, B1, B2, B3, CSU, SNU, CSV, SNV, CSQ, SNQ )

	   LOGICAL	  UPPER

	   REAL 	  A1, A3, B1, B3, CSQ, CSU, CSV

	   COMPLEX	  A2, B2, SNQ, SNU, SNV

PURPOSE

       CLAGS2  computes  2-by-2  unitary  matrices  U, V and Q, such that if ( UPPER ) then U'*A*Q = U'*( A1 A2 )*Q = ( x 0 ) ( 0 A3 ) ( x x ) and
       V'*B*Q = V'*( B1 B2 )*Q = ( x 0 ) ( 0 B3 ) ( x x ) or if ( .NOT.UPPER ) then U'*A*Q = U'*( A1 0 )*Q = ( x x ) ( A2 A3 ) ( 0 x ) and  V'*B*Q
       = V'*( B1 0 )*Q = ( x x ) ( B2 B3 ) ( 0 x ) where U = ( CSU SNU ), V = ( CSV SNV ),	 ( -CONJG(SNU)	CSU )	   ( -CONJG(SNV) CSV )

	 Q = (	   CSQ	    SNQ )
	     ( -CONJG(SNQ)  CSQ )

       Z' denotes the conjugate transpose of Z.

       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.

ARGUMENTS

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

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

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

       CSU     (output) REAL
	       SNU     (output) COMPLEX The desired unitary matrix U.

       CSV     (output) REAL
	       SNV     (output) COMPLEX The desired unitary matrix V.

       CSQ     (output) REAL
	       SNQ     (output) COMPLEX The desired unitary matrix Q.

LAPACK version 3.0						   15 June 2000 							 CLAGS2(l)