Sponsored Content
Top Forums Shell Programming and Scripting diagonal matrix to square matrix Post 302351785 by yifangt on Wednesday 9th of September 2009 01:50:18 PM
Old 09-09-2009
Yes, you are right. The original matrix is NOT a diagonal one. It is upper half symmetric with 1.000 in all the "diagonal" positions.

---------- Post updated at 01:32 PM ---------- Previous update was at 01:30 PM ----------

Thanks, I need to digest your script first. I am just a newbe in shell script and PERL programming.

---------- Post updated at 01:50 PM ---------- Previous update was at 01:32 PM ----------

That's a great solution! Thanks you Tyler!

When I tried to convert my 25000x25000 matrix, I got the "Out of memory!" message and the program stopped. Another problem I noticed is, after I checked the original data, there is ID for each row, i.e.:
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 1.000 0.222 0.451 0.134 0.333
"243906_AT" 1.000 0.112 0.217 0.095
"244908_AT" 1.000 0.508 0.701
"294902_AT" 1.000 0.663
"245902_AT" 1.000

and the output square matrix should be like this:
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 0.234 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 0.435 0.111 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 0.123 0.412 0.205 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 0.012 0.115 0.542 0.587 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 0.102 0.058 0.335 0.159 0.269 1.000 0.222 0.451 0.134 0.333
"243906_AT" 0.325 0.091 0.054 0.357 0.369 0.222 1.000 0.112 0.217 0.095
"244908_AT" 0.412 0.190 0.117 0.258 0.687 0.451 0.112 1.000 0.508 0.701
"294902_AT" 0.087 0.045 0.203 0.654 0.145 0.134 0.217 0.508 1.000 0.663
"245902_AT" 0.098 0.058 0.125 0.341 0.125 0.333 0.095 0.701 0.663 1.000

Then I can retrieve each gene by grep the ID of the first column of each row. I should have posted this information first. Sorry about this. Thanks again Tyler!
 

9 More Discussions You Might Find Interesting

1. Programming

matrix pointer

Can anyone tell me what the following statements do? float (*tab); tab=(float (*)) calloc(MAXCLASS, (MAXCLASS+1)*sizeof(float)); (3 Replies)
Discussion started by: littleboyblu
3 Replies

2. Shell Programming and Scripting

Matrix

Hi All I would like to merge multiple files with the same row and column size into a matrix format In a folder I have multiple files in the following format vi 12.txt a 1 b 5 c 7 d 0 vi 45.txt a 3 b 6 c 9 d 2 vi 9.txt a 4 (7 Replies)
Discussion started by: Lucky Ali
7 Replies

3. Ubuntu

How to convert full data matrix to linearised left data matrix?

Hi all, Is there a way to convert full data matrix to linearised left data matrix? e.g full data matrix Bh1 Bh2 Bh3 Bh4 Bh5 Bh6 Bh7 Bh1 0 0.241058 0.236129 0.244397 0.237479 0.240767 0.245245 Bh2 0.241058 0 0.240594 0.241931 0.241975 ... (8 Replies)
Discussion started by: evoll
8 Replies

4. Shell Programming and Scripting

awk? adjacency matrix to adjacency list / correlation matrix to list

Hi everyone I am very new at awk but think that that might be the best strategy for this. I have a matrix very similar to a correlation matrix and in practical terms I need to convert it into a list containing the values from the matrix (one value per line) with the first field of the line (row... (5 Replies)
Discussion started by: stonemonkey
5 Replies

5. Shell Programming and Scripting

Table to Matrix

Hi, I have a table in the format: 1 0 -1 1 0 2 0 1 -1 0 0 0 3 0 1 1 0 0 0 0 0 0 etc. I am trying to input this to a program, however it is complaining about the fact that it is not in matrix format. How do I add 0's to end of the rows to make them even? Thanks in advance! (2 Replies)
Discussion started by: Rhavin
2 Replies

6. Shell Programming and Scripting

Square matrix to columns

Hello all, I am quite new in this but I need some help to keep going with my analysis. I am struggling with a short script to read a square matrix and convert it in two collumns. A B C D A 0.00 0.06 0.51 0.03 B 0.06 0.00 0.72 0.48 C 0.51 0.72 0.00 ... (7 Replies)
Discussion started by: EvaAM
7 Replies

7. Shell Programming and Scripting

Maybe by AWK: printing help diagonal matrix characters into line

Hi Experts, I want to print this charts diagonal data into straight lines. This is a matrix 24X24 Horizontal and vertical. - I want to print all the diagonal cutting characters into straight line: Data: E F S S A H A L L A T M C N O T S O B O D U Q H I W I B N L O C N I L N L A N S I N... (9 Replies)
Discussion started by: rveri
9 Replies

8. Shell Programming and Scripting

MATRIX to CSV

Hello friends, A big question for the UNIX INTELLIGENCE I have a CSV file as follows: VALUE,USER1,relatedUSER1,relatedUSER2 -1,userA,userB,userC 1,userN,userD,userB 0,userF,userH,userG 0,userT,userH,userB 1,userN,userB,userA -1,userA,userF,userC 0,userF,userH,userG... (15 Replies)
Discussion started by: kraterions
15 Replies

9. UNIX for Beginners Questions & Answers

Matrix multiplication

I have two files. Row id in File1 matches the column id in file2 (starting from column7 )except the last 2 characters. File1 has 50 rows and File 2 has 56 columns. If the id matches I want to multiply the value in column3 of File1 to the entire column in File2. and in the final output print only... (11 Replies)
Discussion started by: Akang
11 Replies
ASCII(7)					       BSD Miscellaneous Information Manual						  ASCII(7)

NAME
ascii -- octal, hexadecimal and decimal ASCII character sets DESCRIPTION
The octal set: 000 nul 001 soh 002 stx 003 etx 004 eot 005 enq 006 ack 007 bel 010 bs 011 ht 012 nl 013 vt 014 np 015 cr 016 so 017 si 020 dle 021 dc1 022 dc2 023 dc3 024 dc4 025 nak 026 syn 027 etb 030 can 031 em 032 sub 033 esc 034 fs 035 gs 036 rs 037 us 040 sp 041 ! 042 " 043 # 044 $ 045 % 046 & 047 ' 050 ( 051 ) 052 * 053 + 054 , 055 - 056 . 057 / 060 0 061 1 062 2 063 3 064 4 065 5 066 6 067 7 070 8 071 9 072 : 073 ; 074 < 075 = 076 > 077 ? 100 @ 101 A 102 B 103 C 104 D 105 E 106 F 107 G 110 H 111 I 112 J 113 K 114 L 115 M 116 N 117 O 120 P 121 Q 122 R 123 S 124 T 125 U 126 V 127 W 130 X 131 Y 132 Z 133 [ 134 135 ] 136 ^ 137 _ 140 ` 141 a 142 b 143 c 144 d 145 e 146 f 147 g 150 h 151 i 152 j 153 k 154 l 155 m 156 n 157 o 160 p 161 q 162 r 163 s 164 t 165 u 166 v 167 w 170 x 171 y 172 z 173 { 174 | 175 } 176 ~ 177 del The hexadecimal set: 00 nul 01 soh 02 stx 03 etx 04 eot 05 enq 06 ack 07 bel 08 bs 09 ht 0a nl 0b vt 0c np 0d cr 0e so 0f si 10 dle 11 dc1 12 dc2 13 dc3 14 dc4 15 nak 16 syn 17 etb 18 can 19 em 1a sub 1b esc 1c fs 1d gs 1e rs 1f us 20 sp 21 ! 22 " 23 # 24 $ 25 % 26 & 27 ' 28 ( 29 ) 2a * 2b + 2c , 2d - 2e . 2f / 30 0 31 1 32 2 33 3 34 4 35 5 36 6 37 7 38 8 39 9 3a : 3b ; 3c < 3d = 3e > 3f ? 40 @ 41 A 42 B 43 C 44 D 45 E 46 F 47 G 48 H 49 I 4a J 4b K 4c L 4d M 4e N 4f O 50 P 51 Q 52 R 53 S 54 T 55 U 56 V 57 W 58 X 59 Y 5a Z 5b [ 5c 5d ] 5e ^ 5f _ 60 ` 61 a 62 b 63 c 64 d 65 e 66 f 67 g 68 h 69 i 6a j 6b k 6c l 6d m 6e n 6f o 70 p 71 q 72 r 73 s 74 t 75 u 76 v 77 w 78 x 79 y 7a z 7b { 7c | 7d } 7e ~ 7f del The decimal set: 0 nul 1 soh 2 stx 3 etx 4 eot 5 enq 6 ack 7 bel 8 bs 9 ht 10 nl 11 vt 12 np 13 cr 14 so 15 si 16 dle 17 dc1 18 dc2 19 dc3 20 dc4 21 nak 22 syn 23 etb 24 can 25 em 26 sub 27 esc 28 fs 29 gs 30 rs 31 us 32 sp 33 ! 34 " 35 # 36 $ 37 % 38 & 39 ' 40 ( 41 ) 42 * 43 + 44 , 45 - 46 . 47 / 48 0 49 1 50 2 51 3 52 4 53 5 54 6 55 7 56 8 57 9 58 : 59 ; 60 < 61 = 62 > 63 ? 64 @ 65 A 66 B 67 C 68 D 69 E 70 F 71 G 72 H 73 I 74 J 75 K 76 L 77 M 78 N 79 O 80 P 81 Q 82 R 83 S 84 T 85 U 86 V 87 W 88 X 89 Y 90 Z 91 [ 92 93 ] 94 ^ 95 _ 96 ` 97 a 98 b 99 c 100 d 101 e 102 f 103 g 104 h 105 i 106 j 107 k 108 l 109 m 110 n 111 o 112 p 113 q 114 r 115 s 116 t 117 u 118 v 119 w 120 x 121 y 122 z 123 { 124 | 125 } 126 ~ 127 del FILES
/usr/share/misc/ascii HISTORY
An ascii manual page appeared in Version 7 AT&T UNIX. BSD
June 5, 1993 BSD
All times are GMT -4. The time now is 06:43 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy