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Full Discussion: Merge multiple tables into big matrix
Top Forums Shell Programming and Scripting Merge multiple tables into big matrix Post 302654353 by newbie83 on Monday 11th of June 2012 03:38:54 PM
Old 06-11-2012
Merge multiple tables into big matrix
Hi all,

I have a complex (beyond my biological expertise) problem at hand.
I need to merge multiple files into 1 big matrix. Please help me with some code.


Inp1
Code:
Ang_0    chr1    98    T    A    
Ang_0    chr1    352    G    A    
Ang_0    chr1    425    C    T    
Ang_0    chr2    471    T    G    
Ang_0    chr2    508    T    -


Inp2
Code:
Bng_0    chr1    98    T    G    
Bng_0    chr1    352    G    A        
Bng_0    chr2    471    T    A    
Bng_0    chr2    508    T    -

Inp3
Code:
Cng_0    chr1    198    T    A    
Cng_0    chr1    352    G    A    
Cng_0    chr1    425    C    T    
Cng_0    chr2    471    T    G


Outp
Code:
            
           Ang_0    Bng_0 Cng_0    
chr1    98    A    G    T
chr1    198    T    T    A
chr1     352    A    A    A
chr1    425    T    C    T
chr2    471    G    A    G
chr2    508    -    -    T



Input files have 5 columns, 1=organism name, 2=chormosome number, 3=chromosome position,4=reference,5=Alternate

First columns 2 and 3 have to be matched in all the input files, if all files have a record for a particular column2 and 3 value
then column5 value has to be outputted. If an input file does not have a record matching a particular column2 and 3 values, column
4 value from any of the input files having that record has to be printed in the output. The column names in the output files
will be the organism name (column 1 of input files.)

I have 123 files and ~30,000 rows in each file.
So the output will have 125 columns, columns 3 through 125 are organism names, column 1 and 2 are chromosome and position.

Please let me know if I am not clear in my requirements. Thanks a lot in advance.
 

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LEARN ABOUT CENTOS

zlag2c

zlag2c.f(3)							      LAPACK							       zlag2c.f(3)

NAME

       zlag2c.f -

SYNOPSIS

   Functions/Subroutines
       subroutine zlag2c (M, N, A, LDA, SA, LDSA, INFO)
	   ZLAG2C converts a complex double precision matrix to a complex single precision matrix.

Function/Subroutine Documentation
   subroutine zlag2c (integerM, integerN, complex*16, dimension( lda, * )A, integerLDA, complex, dimension( ldsa, * )SA, integerLDSA, integerINFO)
       ZLAG2C converts a complex double precision matrix to a complex single precision matrix.

       Purpose:

	    ZLAG2C converts a COMPLEX*16 matrix, SA, to a COMPLEX matrix, A.

	    RMAX is the overflow for the SINGLE PRECISION arithmetic
	    ZLAG2C checks that all the entries of A are between -RMAX and
	    RMAX. If not the convertion is aborted and a flag is raised.

	    This is an auxiliary routine so there is no argument checking.

       Parameters:
	   M

		     M is INTEGER
		     The number of lines of the matrix A.  M >= 0.

	   N

		     N is INTEGER
		     The number of columns of the matrix A.  N >= 0.

	   A

		     A is COMPLEX*16 array, dimension (LDA,N)
		     On entry, the M-by-N coefficient matrix A.

	   LDA

		     LDA is INTEGER
		     The leading dimension of the array A.  LDA >= max(1,M).

	   SA

		     SA is COMPLEX array, dimension (LDSA,N)
		     On exit, if INFO=0, the M-by-N coefficient matrix SA; if
		     INFO>0, the content of SA is unspecified.

	   LDSA

		     LDSA is INTEGER
		     The leading dimension of the array SA.  LDSA >= max(1,M).

	   INFO

		     INFO is INTEGER
		     = 0:  successful exit.
		     = 1:  an entry of the matrix A is greater than the SINGLE
			   PRECISION overflow threshold, in this case, the content
			   of SA in exit is unspecified.

       Author:
	   Univ. of Tennessee

	   Univ. of California Berkeley

	   Univ. of Colorado Denver

	   NAG Ltd.

       Date:
	   September 2012

       Definition at line 108 of file zlag2c.f.

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

Version 3.4.2							  Tue Sep 25 2012						       zlag2c.f(3)
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