1.1 --- a/scripts/last-dotplot Mon Feb 26 08:12:10 2018 +0900
1.2 +++ b/scripts/last-dotplot Mon Mar 05 12:06:48 2018 +0900
1.3 @@ -285,7 +285,7 @@
1.4 return natural_sort_key(oneSeqRanges[0][0])
1.5
1.6 def sizeKey(oneSeqRanges):
1.7 - return sum(b - e for n, b, e in oneSeqRanges), nameKey(oneSeqRanges)
1.8 + return sum(b - e for n, b, e, s in oneSeqRanges), nameKey(oneSeqRanges)
1.9
1.10 def alignmentKey(seqNamesToLists, oneSeqRanges):
1.11 seqName = oneSeqRanges[0][0]
2.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000
2.2 +++ b/test/last-dotplot-test.out Mon Mar 05 12:06:48 2018 +0900
2.3 @@ -0,0 +1,335 @@
2.4 +TEST 102.maf
2.5 +3396982345 3177
2.6 +
2.7 +TEST -v -x600 -c orange -r teal --sort1=2 --border-color=brown 102.maf
2.8 +last-dotplot: font: /usr/share/fonts/liberation/LiberationSans-Regular.ttf
2.9 +last-dotplot: reading alignments...
2.10 +last-dotplot: cutting...
2.11 +last-dotplot: reading secondary alignments...
2.12 +last-dotplot: cutting...
2.13 +last-dotplot: sorting...
2.14 +last-dotplot: chr19 1383883 1383969
2.15 +last-dotplot: chr19 1387780 1388965
2.16 +last-dotplot: chr19 1390828 1391190
2.17 +last-dotplot: chr19 1393213 1393358
2.18 +last-dotplot: chr19 1395360 1395511
2.19 +last-dotplot: chr19 17615403 17615478
2.20 +last-dotplot: chr19 18430532 18430615
2.21 +last-dotplot: chr19 47072174 47072264
2.22 +last-dotplot: chr3 23607529 23607606
2.23 +last-dotplot: chr3 33026597 33026675
2.24 +last-dotplot: chr3 37588349 37588441
2.25 +last-dotplot: chr3 89815452 89815525
2.26 +last-dotplot: chr3 127741348 127741429
2.27 +last-dotplot: chr3 130609381 130609461
2.28 +last-dotplot: chr3 152862866 152862947
2.29 +last-dotplot: chr3 186865624 186865699
2.30 +last-dotplot: chr5 4867398 4867471
2.31 +last-dotplot: chr5 74376550 74376623
2.32 +last-dotplot: chr5 93489515 93489591
2.33 +last-dotplot: chr5 169763588 169763671
2.34 +last-dotplot: chr5 171574427 171574500
2.35 +last-dotplot: chr5 173701172 173701249
2.36 +last-dotplot: chr5 177958514 177958591
2.37 +last-dotplot: chr17 19079582 19079655
2.38 +last-dotplot: chr17 19172423 19172496
2.39 +last-dotplot: chr17 19205764 19205837
2.40 +last-dotplot: chr17 27793612 27793685
2.41 +last-dotplot: chr17 28925902 28925982
2.42 +last-dotplot: chr17 29190042 29190115
2.43 +last-dotplot: chr17 58670463 58670536
2.44 +last-dotplot: chr7 65260279 65260354
2.45 +last-dotplot: chr7 100370569 100370642
2.46 +last-dotplot: chr7 101590352 101590447
2.47 +last-dotplot: chr7 101723218 101723313
2.48 +last-dotplot: chr7 157969496 157969572
2.49 +last-dotplot: chr1 21590603 21590709
2.50 +last-dotplot: chr1 145869990 145870063
2.51 +last-dotplot: chr1 155997846 155997940
2.52 +last-dotplot: chr1 161050878 161050970
2.53 +last-dotplot: chr10 122813007 122813087
2.54 +last-dotplot: chr10 124281367 124281441
2.55 +last-dotplot: chr10 126932842 126932937
2.56 +last-dotplot: chr22 20726561 20726644
2.57 +last-dotplot: chr22 23657463 23657536
2.58 +last-dotplot: chr22 46458773 46458849
2.59 +last-dotplot: chr6 1842804 1842877
2.60 +last-dotplot: chr6 65786074 65786151
2.61 +last-dotplot: chr6 170257674 170257754
2.62 +last-dotplot: chr8 76840831 76840936
2.63 +last-dotplot: chr8 98433234 98433318
2.64 +last-dotplot: chr12 19357508 19357581
2.65 +last-dotplot: chr12 71544959 71545052
2.66 +last-dotplot: chr14 80332102 80332183
2.67 +last-dotplot: chr14 104715645 104715730
2.68 +last-dotplot: chr18 8561181 8561272
2.69 +last-dotplot: chr18 55335065 55335140
2.70 +last-dotplot: chr4 3839035 3839110
2.71 +last-dotplot: chr4 54783677 54783767
2.72 +last-dotplot: chr2 192414435 192414516
2.73 +last-dotplot: chr2 240456604 240456683
2.74 +last-dotplot: chr15 45614722 45614800
2.75 +last-dotplot: chr15 78230458 78230537
2.76 +last-dotplot: chr21 14291153 14291236
2.77 +last-dotplot: chr21 43027907 43027980
2.78 +last-dotplot: chr20 4034120 4034195
2.79 +last-dotplot: chr20 17684717 17684790
2.80 +last-dotplot: chrX 39928389 39928462
2.81 +last-dotplot: chrX 83302574 83302647
2.82 +last-dotplot: chr16 722456 722540
2.83 +last-dotplot: chr11 67464119 67464196
2.84 +last-dotplot: chr13 113342188 113342261
2.85 +last-dotplot:
2.86 +last-dotplot: 102 0 699
2.87 +last-dotplot:
2.88 +last-dotplot: choosing bp per pixel...
2.89 +last-dotplot: choosing bp per pixel...
2.90 +last-dotplot: bp per pixel = 15
2.91 +last-dotplot: width: 581
2.92 +last-dotplot: height: 47
2.93 +last-dotplot: processing alignments...
2.94 +last-dotplot: reading annotations...
2.95 +last-dotplot: drawing...
2.96 +2981739013 1818
2.97 +
2.98 +TEST -v -y30 --max-gap1=0 --pad=0.08 --border-pixels=2 --sort1=3 102.maf
2.99 +last-dotplot: font: /usr/share/fonts/liberation/LiberationSans-Regular.ttf
2.100 +last-dotplot: reading alignments...
2.101 +last-dotplot: cutting...
2.102 +last-dotplot: reading secondary alignments...
2.103 +last-dotplot: cutting...
2.104 +last-dotplot: sorting...
2.105 +last-dotplot: chr16 722428 722568
2.106 +last-dotplot: chr19 1383855 1383997
2.107 +last-dotplot: chr19 1387752 1387902
2.108 +last-dotplot: chr19 1388468 1388648
2.109 +last-dotplot: chr19 1388774 1388993
2.110 +last-dotplot: chr19 1390800 1391218
2.111 +last-dotplot: chr19 1393185 1393386
2.112 +last-dotplot: chr19 1395332 1395539
2.113 +last-dotplot: chr19 17615375 17615506
2.114 +last-dotplot: chr19 18430504 18430643
2.115 +last-dotplot: chr19 47072146 47072292
2.116 +last-dotplot: chr8 76840803 76840964
2.117 +last-dotplot: chr8 98433206 98433346
2.118 +last-dotplot: chr20 4034092 4034223
2.119 +last-dotplot: chr20 17684689 17684818
2.120 +last-dotplot: chr4 3839007 3839138
2.121 +last-dotplot: chr4 54783649 54783795
2.122 +last-dotplot: chr12 19357480 19357609
2.123 +last-dotplot: chr12 71544931 71545080
2.124 +last-dotplot: chr18 8561153 8561300
2.125 +last-dotplot: chr18 55335037 55335168
2.126 +last-dotplot: chr7 65260251 65260382
2.127 +last-dotplot: chr7 100370541 100370670
2.128 +last-dotplot: chr7 101590324 101590475
2.129 +last-dotplot: chr7 101723190 101723341
2.130 +last-dotplot: chr7 157969468 157969600
2.131 +last-dotplot: chr13 113342160 113342289
2.132 +last-dotplot: chr17 19079554 19079683
2.133 +last-dotplot: chr17 19172395 19172524
2.134 +last-dotplot: chr17 19205736 19205865
2.135 +last-dotplot: chr17 27793584 27793713
2.136 +last-dotplot: chr17 28925874 28926010
2.137 +last-dotplot: chr17 29190014 29190143
2.138 +last-dotplot: chr17 58670435 58670564
2.139 +last-dotplot: chr22 20726533 20726672
2.140 +last-dotplot: chr22 23657435 23657564
2.141 +last-dotplot: chr22 46458745 46458877
2.142 +last-dotplot: chr6 1842776 1842905
2.143 +last-dotplot: chr6 65786046 65786179
2.144 +last-dotplot: chr6 170257646 170257782
2.145 +last-dotplot: chr5 4867370 4867499
2.146 +last-dotplot: chr5 74376522 74376651
2.147 +last-dotplot: chr5 93489487 93489619
2.148 +last-dotplot: chr5 169763560 169763699
2.149 +last-dotplot: chr5 171574399 171574528
2.150 +last-dotplot: chr5 173701144 173701277
2.151 +last-dotplot: chr5 177958486 177958619
2.152 +last-dotplot: chr1 21590575 21590737
2.153 +last-dotplot: chr1 145869962 145870091
2.154 +last-dotplot: chr1 155997818 155997968
2.155 +last-dotplot: chr1 161050850 161050998
2.156 +last-dotplot: chr11 67464091 67464224
2.157 +last-dotplot: chr14 80332074 80332211
2.158 +last-dotplot: chr14 104715617 104715758
2.159 +last-dotplot: chr3 23607501 23607634
2.160 +last-dotplot: chr3 33026569 33026703
2.161 +last-dotplot: chr3 37588321 37588469
2.162 +last-dotplot: chr3 89815424 89815553
2.163 +last-dotplot: chr3 127741320 127741457
2.164 +last-dotplot: chr3 130609353 130609489
2.165 +last-dotplot: chr3 152862838 152862975
2.166 +last-dotplot: chr3 186865596 186865727
2.167 +last-dotplot: chr2 192414407 192414544
2.168 +last-dotplot: chr2 240456576 240456711
2.169 +last-dotplot: chr15 45614694 45614828
2.170 +last-dotplot: chr15 78230430 78230565
2.171 +last-dotplot: chr10 122812979 122813115
2.172 +last-dotplot: chr10 124281339 124281469
2.173 +last-dotplot: chr10 126932814 126932965
2.174 +last-dotplot: chr21 14291125 14291264
2.175 +last-dotplot: chr21 43027879 43028008
2.176 +last-dotplot: chrX 39928361 39928490
2.177 +last-dotplot: chrX 83302546 83302675
2.178 +last-dotplot:
2.179 +last-dotplot: 102 0 699
2.180 +last-dotplot:
2.181 +last-dotplot: choosing bp per pixel...
2.182 +last-dotplot: choosing bp per pixel...
2.183 +last-dotplot: bp per pixel = 24
2.184 +last-dotplot: width: 619
2.185 +last-dotplot: height: 30
2.186 +last-dotplot: processing alignments...
2.187 +last-dotplot: reading annotations...
2.188 +last-dotplot: drawing...
2.189 +3953352818 1272
2.190 +
2.191 +TEST -v --sort2=3 bs100.maf
2.192 +last-dotplot: font: /usr/share/fonts/liberation/LiberationSans-Regular.ttf
2.193 +last-dotplot: reading alignments...
2.194 +last-dotplot: cutting...
2.195 +last-dotplot: reading secondary alignments...
2.196 +last-dotplot: cutting...
2.197 +last-dotplot: sorting...
2.198 +last-dotplot: chrM 0 16571
2.199 +last-dotplot:
2.200 +last-dotplot: 55 0 87
2.201 +last-dotplot: 21 0 87
2.202 +last-dotplot: 95 0 87
2.203 +last-dotplot: 7 0 87
2.204 +last-dotplot: 16 0 87
2.205 +last-dotplot: 97 0 87
2.206 +last-dotplot: 88 0 87
2.207 +last-dotplot: 28 0 87
2.208 +last-dotplot: 25 0 87
2.209 +last-dotplot: 13 0 87
2.210 +last-dotplot: 1 0 87
2.211 +last-dotplot: 90 0 87
2.212 +last-dotplot: 83 0 87
2.213 +last-dotplot: 31 0 87
2.214 +last-dotplot: 23 0 87
2.215 +last-dotplot: 12 0 87
2.216 +last-dotplot: 34 0 87
2.217 +last-dotplot: 10 0 87
2.218 +last-dotplot: 38 0 87
2.219 +last-dotplot: 91 0 87
2.220 +last-dotplot: 93 0 87
2.221 +last-dotplot: 96 0 87
2.222 +last-dotplot: 76 0 87
2.223 +last-dotplot: 74 0 87
2.224 +last-dotplot: 26 0 87
2.225 +last-dotplot: 29 0 87
2.226 +last-dotplot: 35 0 87
2.227 +last-dotplot: 8 0 87
2.228 +last-dotplot: 40 0 87
2.229 +last-dotplot: 42 0 87
2.230 +last-dotplot: 69 0 87
2.231 +last-dotplot: 4 0 87
2.232 +last-dotplot: 20 0 87
2.233 +last-dotplot: 92 0 87
2.234 +last-dotplot: 50 0 87
2.235 +last-dotplot: 30 0 87
2.236 +last-dotplot: 5 0 87
2.237 +last-dotplot: 48 0 87
2.238 +last-dotplot: 47 0 87
2.239 +last-dotplot: 75 0 87
2.240 +last-dotplot: 54 0 87
2.241 +last-dotplot: 44 0 87
2.242 +last-dotplot: 14 0 87
2.243 +last-dotplot: 98 0 87
2.244 +last-dotplot: 70 0 87
2.245 +last-dotplot: 39 0 87
2.246 +last-dotplot: 9 0 87
2.247 +last-dotplot: 32 0 87
2.248 +last-dotplot: 81 0 87
2.249 +last-dotplot: 89 0 87
2.250 +last-dotplot: 99 0 87
2.251 +last-dotplot: 86 0 87
2.252 +last-dotplot: 67 0 87
2.253 +last-dotplot: 56 0 87
2.254 +last-dotplot: 51 0 87
2.255 +last-dotplot: 45 0 87
2.256 +last-dotplot: 82 0 87
2.257 +last-dotplot: 59 0 87
2.258 +last-dotplot: 24 0 87
2.259 +last-dotplot: 37 0 87
2.260 +last-dotplot: 41 0 87
2.261 +last-dotplot: 52 0 87
2.262 +last-dotplot: 18 0 87
2.263 +last-dotplot: 77 0 87
2.264 +last-dotplot: 79 0 87
2.265 +last-dotplot: 72 0 87
2.266 +last-dotplot: 6 0 87
2.267 +last-dotplot: 57 0 87
2.268 +last-dotplot: 85 0 87
2.269 +last-dotplot: 78 0 87
2.270 +last-dotplot: 65 0 87
2.271 +last-dotplot: 94 0 87
2.272 +last-dotplot: 2 0 87
2.273 +last-dotplot: 3 0 87
2.274 +last-dotplot: 46 0 87
2.275 +last-dotplot: 60 0 87
2.276 +last-dotplot: 58 0 87
2.277 +last-dotplot: 33 0 87
2.278 +last-dotplot: 15 0 87
2.279 +last-dotplot: 49 0 87
2.280 +last-dotplot: 64 0 87
2.281 +last-dotplot: 0 0 87
2.282 +last-dotplot: 27 0 87
2.283 +last-dotplot: 19 0 87
2.284 +last-dotplot: 43 0 87
2.285 +last-dotplot: 53 0 87
2.286 +last-dotplot: 36 0 87
2.287 +last-dotplot: 73 0 87
2.288 +last-dotplot: 66 0 87
2.289 +last-dotplot: 87 0 87
2.290 +last-dotplot: 22 0 87
2.291 +last-dotplot: 71 0 87
2.292 +last-dotplot: 68 0 87
2.293 +last-dotplot: 11 0 87
2.294 +last-dotplot: 63 0 87
2.295 +last-dotplot:
2.296 +last-dotplot: choosing bp per pixel...
2.297 +last-dotplot: choosing bp per pixel...
2.298 +last-dotplot: bp per pixel = 17
2.299 +last-dotplot: width: 975
2.300 +last-dotplot: height: 664
2.301 +last-dotplot: processing alignments...
2.302 +last-dotplot: reading annotations...
2.303 +last-dotplot: drawing...
2.304 +833292477 18662
2.305 +
2.306 +TEST -v -2? --sort2=0 --strands2=1 bs100.maf
2.307 +last-dotplot: font: /usr/share/fonts/liberation/LiberationSans-Regular.ttf
2.308 +last-dotplot: reading alignments...
2.309 +last-dotplot: cutting...
2.310 +last-dotplot: reading secondary alignments...
2.311 +last-dotplot: cutting...
2.312 +last-dotplot: sorting...
2.313 +last-dotplot: chrM 0 1663
2.314 +last-dotplot: chrM 4973 6206
2.315 +last-dotplot: chrM 7868 8021
2.316 +last-dotplot: chrM 11073 14033
2.317 +last-dotplot:
2.318 +last-dotplot: 0 0 87 -
2.319 +last-dotplot: 1 0 87 +
2.320 +last-dotplot: 2 0 87 +
2.321 +last-dotplot: 3 0 87 -
2.322 +last-dotplot: 4 0 87 +
2.323 +last-dotplot: 5 0 87 -
2.324 +last-dotplot: 6 0 87 +
2.325 +last-dotplot: 7 0 87 -
2.326 +last-dotplot: 8 0 87 +
2.327 +last-dotplot: 9 0 87 +
2.328 +last-dotplot:
2.329 +last-dotplot: choosing bp per pixel...
2.330 +last-dotplot: choosing bp per pixel...
2.331 +last-dotplot: bp per pixel = 7
2.332 +last-dotplot: width: 863
2.333 +last-dotplot: height: 139
2.334 +last-dotplot: processing alignments...
2.335 +last-dotplot: reading annotations...
2.336 +last-dotplot: drawing...
2.337 +2996486939 3971
2.338 +
3.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000
3.2 +++ b/test/last-dotplot-test.sh Mon Mar 05 12:06:48 2018 +0900
3.3 @@ -0,0 +1,25 @@
3.4 +#! /bin/sh
3.5 +
3.6 +cd $(dirname $0)
3.7 +
3.8 +PATH=../scripts:$PATH
3.9 +
3.10 +png=/tmp/$$.png
3.11 +
3.12 +trap 'rm -f "$png"' EXIT
3.13 +
3.14 +plotSum () {
3.15 + echo TEST "$@"
3.16 + last-dotplot -s0 "$@" "$png"
3.17 + cksum < "$png"
3.18 + echo
3.19 +}
3.20 +
3.21 +{
3.22 + plotSum 102.maf
3.23 + plotSum -v -x600 -c orange -r teal --sort1=2 --border-color=brown 102.maf
3.24 + plotSum -v -y30 --max-gap1=0 --pad=0.08 --border-pixels=2 --sort1=3 102.maf
3.25 + plotSum -v --sort2=3 bs100.maf
3.26 + plotSum -v -2'?' --sort2=0 --strands2=1 bs100.maf
3.27 +} 2>&1 |
3.28 +diff -u $(basename $0 .sh).out -