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!
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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