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Top Forums Shell Programming and Scripting awk to convert table-by-row to matrix table Post 302881907 by yifangt on Thursday 2nd of January 2014 05:31:12 PM
Old 01-02-2014
additional: mark missing data with -

Thank you both!
Amazing scripts!
disedorgue, Your script is what i was thinking to use, but need more digestion.
More challenging with real data, that some members (i.e. columns) of some site are with missing data as indicated with "-" in previous post, but not listed in the infile, which will be assigned with an empty cell and will cause confusion.
Code:
infile: 
site1 A:o,p,q,r,s,t
site1 C:y,u
site1 T:v,w
site1 -:x,z
site2 A:p,r,t,v,w,z
site2 C:u,y
site2 G:q,s
site3 A:o,q,s,t,u,z
site3 C:y
site3 T:v,w,x

Code:
output:
SITE    o p q r s t u v w x y z 
site1    A A A A A A C T T - C - 
site2     A G A G A C A A  C A 
site3    A  A  A A A T T T C A

How to add "-" to those "empty" cells so that the table is aligned? Thanks a lot again!

Last edited by yifangt; 01-02-2014 at 06:35 PM.. Reason: typo
 

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SGEEQU(l)								 )								 SGEEQU(l)

NAME
SGEEQU - compute row and column scalings intended to equilibrate an M-by-N matrix A and reduce its condition number SYNOPSIS
SUBROUTINE SGEEQU( M, N, A, LDA, R, C, ROWCND, COLCND, AMAX, INFO ) INTEGER INFO, LDA, M, N REAL AMAX, COLCND, ROWCND REAL A( LDA, * ), C( * ), R( * ) PURPOSE
SGEEQU computes row and column scalings intended to equilibrate an M-by-N matrix A and reduce its condition number. R returns the row scale factors and C the column scale factors, chosen to try to make the largest element in each row and column of the matrix B with elements B(i,j)=R(i)*A(i,j)*C(j) have absolute value 1. R(i) and C(j) are restricted to be between SMLNUM = smallest safe number and BIGNUM = largest safe number. Use of these scaling factors is not guaranteed to reduce the condition number of A but works well in practice. ARGUMENTS
M (input) INTEGER The number of rows of the matrix A. M >= 0. N (input) INTEGER The number of columns of the matrix A. N >= 0. A (input) REAL array, dimension (LDA,N) The M-by-N matrix whose equilibration factors are to be computed. LDA (input) INTEGER The leading dimension of the array A. LDA >= max(1,M). R (output) REAL array, dimension (M) If INFO = 0 or INFO > M, R contains the row scale factors for A. C (output) REAL array, dimension (N) If INFO = 0, C contains the column scale factors for A. ROWCND (output) REAL If INFO = 0 or INFO > M, ROWCND contains the ratio of the smallest R(i) to the largest R(i). If ROWCND >= 0.1 and AMAX is neither too large nor too small, it is not worth scaling by R. COLCND (output) REAL If INFO = 0, COLCND contains the ratio of the smallest C(i) to the largest C(i). If COLCND >= 0.1, it is not worth scaling by C. AMAX (output) REAL Absolute value of largest matrix element. If AMAX is very close to overflow or very close to underflow, the matrix should be scaled. INFO (output) INTEGER = 0: successful exit < 0: if INFO = -i, the i-th argument had an illegal value > 0: if INFO = i, and i is <= M: the i-th row of A is exactly zero > M: the (i-M)-th column of A is exactly zero LAPACK version 3.0 15 June 2000 SGEEQU(l)
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