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Top Forums Shell Programming and Scripting Chromosomal Bin Size Adjustment Post 302968951 by jacobs.smith on Wednesday 16th of March 2016 11:52:26 AM
Old 03-16-2016
Chromosomal Bin Size Adjustment

Dear All,

Hope you are rocking.

I was using publicly available tools to do a task to chop a region into equal number of bins. But the glitch with this tool is that it causes the last region to carry lower number of bases than requested. But I want the first bin to have the lower ones.

Here is the input

Code:
cat input
chr1 100 225 name

When I ask to give me bins such that each bin size is 10bases, the current tool gives output this way

Code:
chr1 100 110 name1
chr1 110 120 name2
chr1 120 130 name3
chr1 130 140 name4
chr1 140 150 name5
chr1 150 160 name6
chr1 160 170 name7
chr1 170 180 name8
chr1 180 190 name9
chr1 190 200 name10
chr1 200 210 name11
chr1 210 220 name12
chr1 220 225 name12

If you see the last record, it is only 5bases long
Code:
chr1 220 225 name12

But I want this record to be 10bases long and the first record
Code:
chr1 100 110 name1

to be 5bases.


So my new output becomes

Code:
chr1 100 105
chr1 105 115
chr1 115 125
chr1 125 135
chr1 135 145
chr1 145 155
chr1 155 165
chr1 165 175
chr1 175 185
chr1 185 195
chr1 195 205
chr1 205 215
chr1 215 225

Thank you in advance
 

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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
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