/usr/share/bedtools/test/reldist/test-reldist.sh is in bedtools-test 2.25.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 | #!/bin/bash
BT=${BT-../../bin/bedtools}
DATA=${DATA-../../data}
check()
{
if diff $1 $2; then
echo ok
else
echo fail
fi
}
###########################################################
# Test a basic self intersection. The relative distances
# should all be 0 in this case.
############################################################
echo " reldist.t01...\c"
echo \
"reldist count total fraction
0.00 43424 43424 1.000" > exp
$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \
-b $DATA/refseq.chr1.exons.bed.gz > obs
check obs exp
rm obs exp
###########################################################
# Test intervaks that are randomly distributed.
# The relative distances should equally represented .
############################################################
echo " reldist.t02...\c"
echo \
"reldist count total fraction
0.00 164 43408 0.004
0.01 551 43408 0.013
0.02 598 43408 0.014
0.03 637 43408 0.015
0.04 793 43408 0.018
0.05 688 43408 0.016
0.06 874 43408 0.020
0.07 765 43408 0.018
0.08 685 43408 0.016
0.09 929 43408 0.021
0.10 876 43408 0.020
0.11 959 43408 0.022
0.12 860 43408 0.020
0.13 851 43408 0.020
0.14 903 43408 0.021
0.15 893 43408 0.021
0.16 883 43408 0.020
0.17 828 43408 0.019
0.18 917 43408 0.021
0.19 875 43408 0.020
0.20 897 43408 0.021
0.21 986 43408 0.023
0.22 903 43408 0.021
0.23 944 43408 0.022
0.24 904 43408 0.021
0.25 867 43408 0.020
0.26 943 43408 0.022
0.27 933 43408 0.021
0.28 1132 43408 0.026
0.29 881 43408 0.020
0.30 851 43408 0.020
0.31 963 43408 0.022
0.32 950 43408 0.022
0.33 965 43408 0.022
0.34 907 43408 0.021
0.35 884 43408 0.020
0.36 965 43408 0.022
0.37 944 43408 0.022
0.38 911 43408 0.021
0.39 939 43408 0.022
0.40 921 43408 0.021
0.41 950 43408 0.022
0.42 935 43408 0.022
0.43 919 43408 0.021
0.44 915 43408 0.021
0.45 934 43408 0.022
0.46 843 43408 0.019
0.47 850 43408 0.020
0.48 1006 43408 0.023
0.49 937 43408 0.022" > exp
$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \
-b $DATA/aluY.chr1.bed.gz > obs
check obs exp
rm obs exp
###########################################################
# Test intervaks that are consistently closer to one another
# than expected. The distances should be biased towards 0.=
############################################################
echo " reldist.t03...\c"
echo \
"reldist count total fraction
0.00 20629 43422 0.475
0.01 2629 43422 0.061
0.02 1427 43422 0.033
0.03 985 43422 0.023
0.04 897 43422 0.021
0.05 756 43422 0.017
0.06 667 43422 0.015
0.07 557 43422 0.013
0.08 603 43422 0.014
0.09 487 43422 0.011
0.10 461 43422 0.011
0.11 423 43422 0.010
0.12 427 43422 0.010
0.13 435 43422 0.010
0.14 375 43422 0.009
0.15 367 43422 0.008
0.16 379 43422 0.009
0.17 371 43422 0.009
0.18 346 43422 0.008
0.19 389 43422 0.009
0.20 377 43422 0.009
0.21 411 43422 0.009
0.22 377 43422 0.009
0.23 352 43422 0.008
0.24 334 43422 0.008
0.25 315 43422 0.007
0.26 370 43422 0.009
0.27 330 43422 0.008
0.28 330 43422 0.008
0.29 280 43422 0.006
0.30 309 43422 0.007
0.31 326 43422 0.008
0.32 287 43422 0.007
0.33 294 43422 0.007
0.34 306 43422 0.007
0.35 307 43422 0.007
0.36 309 43422 0.007
0.37 271 43422 0.006
0.38 293 43422 0.007
0.39 311 43422 0.007
0.40 331 43422 0.008
0.41 320 43422 0.007
0.42 299 43422 0.007
0.43 327 43422 0.008
0.44 321 43422 0.007
0.45 326 43422 0.008
0.46 306 43422 0.007
0.47 354 43422 0.008
0.48 365 43422 0.008
0.49 336 43422 0.008
0.50 38 43422 0.001" > exp
$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \
-b $DATA/gerp.chr1.bed.gz > obs
check obs exp
rm obs exp
|