Extract values from a matrix given the rows and columns
Hi All,
I have a huge (and its really huge!) matrix about 400GB in size (2 million rows by 1.5 million columns) . I am trying to optimize its space by creating a sparse representation of it.
Miniature version of the matrix looks like this (matrix.mtx):
So, this is what I have done until now.
1. I got the important rows and columns from another means not by processing this great matrix, those rows and columns which I really care about, and have those rows and columns stored in another text file called row_column.tmp
My row_column.tmp looks like this:
So, this means first row and first column is really important to me and I would like to extract the value from the huge matrix and make my output file look like this:
output.mtx
The above output shows that by reading in the rows and columns from the row_column.tmp, I go to the main matrix file matrix.mtx and extract the value from that particular row and column and put the value against that row and column in my output.mtx file.
Things which I need to care about is that I should not load the entire matrix in memory else things will get really messy. I am using Linux with BASH.
Hi guys I want to print the values by using this script but its giving the no of rows and columns as input instead of values
Would you plz help me on this
FILE- chr1.txt
1981 1
1971 1
1961 1
1941 1
perl script
#!/usr/bin/perl -w
$infile1 = 'chr1.txt';
$outfile3 = 'out3.txt';
... (3 Replies)
Hello guys,
Please help me to solve this problem. I have tried some awk commands but couldn't succeed.
I have a tab delimited file where each record is separated by ------ and 4th column of each record is same.
<INPUT FILE>
------
peon 53931587 53931821 ... (12 Replies)
Hi
My pipe delimited .txt file contains rows with 10 columns.
Can anyone advise how I output to file only those rows with the letters ‘ci'
as the first 2 characters in the 3rd column ?
Many thanks (4 Replies)
Hello,
I want to extract several columns and rows from a huge tab delimited file
for example: I want to print from from column 3 to 68 till row number 30.
I have tried using cut command but it was extracting whole 3rd and 68th column.
Please suggest a solution.
Ryan (8 Replies)
Hi all,
I have a large matrix of 720 x 25. I want to get sum of range of rows and columns. Like, I need sum of all columns and row number 2 to 21, then leaving 22nd row, again sum of all columns and row number 23 to 42 again leaving 43rd row and then sum of 44th to 63. Means I want to add all... (4 Replies)
Hi I have a matrix with n rows and m columns like below example. i want to extract all the pairs with values <200.
Input
A B C D
A 100 206 51 300
B 206 100 72 48
C 351 22 100 198
D 13 989 150 100
Output format
A,A:200
A,C:51
B,B:100... (2 Replies)
Hi all, I'm pretty much a newbie to UNIX. I would appreciate any help with UNIX coding on comparing two large csv files (greater than 10 GB in size), and output a file with matching columns.
I want to compare file1 and file2 by 'id' and 'chain' columns, then extract exact matching rows'... (5 Replies)
Hallo,
I would need to extract only rows which has different value in the second and third column.
Thank you very much for any advices
Input:
A 0 0
B 0 1
C 1 1
D 1 3
Output
B 0 1
D 1 3 (4 Replies)
Hello
I have a file like this:
> cat examplefile
ghi|NN603762|eee
mno|NN607265|ttt
pqr|NN613879|yyy
stu|NN615002|uuu
jkl|NN607265|rrr
vwx|NN615002|iii
yzA|NN618555|ooo
def|NN190486|www
BCD|NN628717|ppp
abc|NN190486|qqq
EFG|NN628717|aaa
HIJ|NN628717|sss
>
I can sort the file by... (5 Replies)
Discussion started by: CHoggarth
5 Replies
LEARN ABOUT REDHAT
slaqgb
SLAQGB(l) ) SLAQGB(l)
NAME
SLAQGB - equilibrate a general M by N band matrix A with KL subdiagonals and KU superdiagonals using the row and scaling factors in the
vectors R and C
SYNOPSIS
SUBROUTINE SLAQGB( M, N, KL, KU, AB, LDAB, R, C, ROWCND, COLCND, AMAX, EQUED )
CHARACTER EQUED
INTEGER KL, KU, LDAB, M, N
REAL AMAX, COLCND, ROWCND
REAL AB( LDAB, * ), C( * ), R( * )
PURPOSE
SLAQGB equilibrates a general M by N band matrix A with KL subdiagonals and KU superdiagonals using the row and scaling factors in the vec-
tors R and C.
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.
KL (input) INTEGER
The number of subdiagonals within the band of A. KL >= 0.
KU (input) INTEGER
The number of superdiagonals within the band of A. KU >= 0.
AB (input/output) REAL array, dimension (LDAB,N)
On entry, the matrix A in band storage, in rows 1 to KL+KU+1. The j-th column of A is stored in the j-th column of the array AB as
follows: AB(ku+1+i-j,j) = A(i,j) for max(1,j-ku)<=i<=min(m,j+kl)
On exit, the equilibrated matrix, in the same storage format as A. See EQUED for the form of the equilibrated matrix.
LDAB (input) INTEGER
The leading dimension of the array AB. LDA >= KL+KU+1.
R (output) REAL array, dimension (M)
The row scale factors for A.
C (output) REAL array, dimension (N)
The column scale factors for A.
ROWCND (output) REAL
Ratio of the smallest R(i) to the largest R(i).
COLCND (output) REAL
Ratio of the smallest C(i) to the largest C(i).
AMAX (input) REAL
Absolute value of largest matrix entry.
EQUED (output) CHARACTER*1
Specifies the form of equilibration that was done. = 'N': No equilibration
= 'R': Row equilibration, i.e., A has been premultiplied by diag(R). = 'C': Column equilibration, i.e., A has been postmulti-
plied by diag(C). = 'B': Both row and column equilibration, i.e., A has been replaced by diag(R) * A * diag(C).
PARAMETERS
THRESH is a threshold value used to decide if row or column scaling should be done based on the ratio of the row or column scaling factors.
If ROWCND < THRESH, row scaling is done, and if COLCND < THRESH, column scaling is done.
LARGE and SMALL are threshold values used to decide if row scaling should be done based on the absolute size of the largest matrix element.
If AMAX > LARGE or AMAX < SMALL, row scaling is done.
LAPACK version 3.0 15 June 2000 SLAQGB(l)