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Merge pull request #56 from pbelmann/feature/verify-taxonomic-binning
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feature verify taxonomic binning benchmakr
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@pbelmann
pbelmann committed Oct 27, 2015
2 parents 1ffc4d7 + 89e0a7b commit 3b13fc6
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,8 @@ project adheres to [Semantic Versioning](http://semver.org/).
An additional flag `--no-rm` was added to override this and keep
the container after use.

* Verify taxonomic binning benchmark container.

### Fixed

* Fixed bug where passing full paths as the input arguments would cause a
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2,297 changes: 2,297 additions & 0 deletions biobox_cli/verification/data/taxonomic_binning/contigs.fna
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97 changes: 97 additions & 0 deletions biobox_cli/verification/data/taxonomic_binning/labels.binning
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#Bioboxes binning format at http://bioboxes.org/
@Version:0.9.1
@SampleID:bioboxes-validation-dataset
@TaxonomyID:13e21ba783e8aabf730b783276858958

@@SEQUENCEID TAXID
S|S1|C10029 370895
S|S1|C10001 370895
S|S1|C10020 370895
S|S1|C10026 370895
S|S1|C10030 370895
S|S1|C10077 1045854
S|S1|C1001 1009708
S|S1|C10035 1009708
S|S1|C10000 1009708
S|S1|C10 1009708
S|S1|C1005 1009708
S|S1|C0 1394711
S|S1|C10047 1394711
S|S1|C10010 1394711
S|S1|C10078 1263006
S|S1|C10056 1263006
S|S1|C10066 1263006
S|S1|C10040 1263006
S|S1|C10057 1263006
S|S1|C10041 1263006
S|S1|C10009 1263006
S|S1|C10061 1263006
S|S1|C10024 1263006
S|S1|C10028 1263006
S|S1|C10071 1263006
S|S1|C10012 1229484
S|S1|C10044 742723
S|S1|C10036 349101
S|S1|C10076 349101
S|S1|C10032 349101
S|S1|C10031 349101
S|S1|C10021 349101
S|S1|C10043 349101
S|S1|C10013 349101
S|S1|C10037 349101
S|S1|C10014 349101
S|S1|C10050 349101
S|S1|C10002 349101
S|S1|C1008 349101
S|S1|C1004 1230476
S|S1|C10019 1230476
S|S1|C1000 1230476
S|S1|C10064 1230476
S|S1|C10065 1230476
S|S1|C10018 1230476
S|S1|C1002 1230476
S|S1|C10005 1230476
S|S1|C10053 1230476
S|S1|C10004 1230476
S|S1|C10003 1230476
S|S1|C10048 1230476
S|S1|C10058 1230476
S|S1|C10017 1230476
S|S1|C10039 1230476
S|S1|C1 1230476
S|S1|C1006 1230476
S|S1|C10045 1230476
S|S1|C10079 1230476
S|S1|C10027 1230476
S|S1|C10074 1230476
S|S1|C10063 1230476
S|S1|C10051 1230476
S|S1|C10033 1230476
S|S1|C10052 434085
S|S1|C1007 434085
S|S1|C10072 434085
S|S1|C10073 1174684
S|S1|C10069 1174684
S|S1|C10008 1174684
S|S1|C10055 1174684
S|S1|C10067 1174684
S|S1|C10075 1174684
S|S1|C10070 1174684
S|S1|C10059 1174684
S|S1|C10006 1174684
S|S1|C10023 1412874
S|S1|C10062 939301
S|S1|C10016 939301
S|S1|C10046 939301
S|S1|C10060 939301
S|S1|C100 939301
S|S1|C10025 939301
S|S1|C10015 939301
S|S1|C10038 939301
S|S1|C10011 939301
S|S1|C10022 1235799
S|S1|C10007 245012
S|S1|C1003 245012
S|S1|C10080 245012
S|S1|C10068 245012
S|S1|C10034 245012
100 changes: 100 additions & 0 deletions biobox_cli/verification/data/taxonomic_binning/prediction.binning
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# This is the bioboxes.org binning output format at
# https://github.com/bioboxes/rfc/tree/master/data-format

@Version:0.9.1
@SampleID:bioboxes-validation-dataset
@TaxonomyID:13e21ba783e8aabf730b783276858958
@_TaxatorTK_Version:1.3

@@SequenceID TaxID _TaxatorTK_Support _TaxatorTK_Length
S|S1|C0 1 186 186
S|S1|C1 374 511 617
S|S1|C10 1 100 100
S|S1|C100 1 621 621
S|S1|C1000 1 174 180
S|S1|C10000 28211 949 949
S|S1|C10001 32008 3051 3051
S|S1|C10002 1060 229 229
S|S1|C10003 374 367 391
S|S1|C10004 374 269 302
S|S1|C10005 1 100 100
S|S1|C10006 165697 156 156
S|S1|C10007 186802 500 500
S|S1|C10008 1 239 239
S|S1|C10009 1 199 199
S|S1|C1001 28211 595 595
S|S1|C10010 1 334 334
S|S1|C10011 1 236 236
S|S1|C10012 28211 38741 38741
S|S1|C10013 1 605 605
S|S1|C10014 1060 100 100
S|S1|C10015 1 183 183
S|S1|C10016 1 456 456
S|S1|C10017 41294 328 369
S|S1|C10018 374 226 238
S|S1|C10019 374 651 705
S|S1|C1002 374 194 207
S|S1|C10020 13373 7443 7443
S|S1|C10021 1063 455 455
S|S1|C10022 186803 1380 1380
S|S1|C10023 2157 22875 22875
S|S1|C10024 1239 751 751
S|S1|C10025 1 201 201
S|S1|C10026 13373 9566 9566
S|S1|C10027 1 288 288
S|S1|C10028 1 168 168
S|S1|C10029 32008 1154 1154
S|S1|C1003 186802 707 707
S|S1|C10030 13373 5574 5574
S|S1|C10031 1063 625 625
S|S1|C10032 1063 280 280
S|S1|C10033 1 462 494
S|S1|C10034 186802 405 405
S|S1|C10035 1 100 100
S|S1|C10036 1063 184 184
S|S1|C10037 1063 271 271
S|S1|C10038 1 189 189
S|S1|C10039 374 174 182
S|S1|C1004 374 155 160
S|S1|C10040 1 259 259
S|S1|C10041 1 311 311
S|S1|C10043 1063 283 283
S|S1|C10044 1 238 238
S|S1|C10045 374 280 332
S|S1|C10046 1 163 163
S|S1|C10047 1 141 141
S|S1|C10048 374 444 508
S|S1|C1005 1 1217 1217
S|S1|C10050 1063 499 499
S|S1|C10051 374 741 822
S|S1|C10052 1236 4845 4845
S|S1|C10053 374 165 172
S|S1|C10055 165697 1542 1542
S|S1|C10056 1 150 150
S|S1|C10057 1 100 100
S|S1|C10058 1 440 541
S|S1|C10059 165697 931 931
S|S1|C1006 374 436 461
S|S1|C10060 1 171 171
S|S1|C10061 1 382 382
S|S1|C10062 1 309 309
S|S1|C10063 374 431 483
S|S1|C10064 374 522 572
S|S1|C10065 1 186 186
S|S1|C10066 1239 193 193
S|S1|C10067 165697 596 596
S|S1|C10068 186802 433 433
S|S1|C10069 165697 270 270
S|S1|C1007 1236 2621 2621
S|S1|C10070 165697 336 336
S|S1|C10071 1 328 328
S|S1|C10072 1236 1780 1780
S|S1|C10073 1 700 700
S|S1|C10074 1 99 161
S|S1|C10075 41297 962 962
S|S1|C10076 1060 196 196
S|S1|C10077 1 372 372
S|S1|C10078 1239 410 410
S|S1|C10079 1 248 248
S|S1|C1008 1063 233 233
S|S1|C10080 186802 188 188
58 changes: 58 additions & 0 deletions biobox_cli/verification/data/taxonomic_binning/taxonomy/names.dmp
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1 | root | | scientific name |
2 | Bacteria | Bacteria <prokaryote> | scientific name |
356 | Rhizobiales | | scientific name |
374 | Bradyrhizobium | | scientific name |
1060 | Rhodobacter | | scientific name |
1063 | Rhodobacter sphaeroides | | scientific name |
1224 | Proteobacteria | | scientific name |
1236 | Gammaproteobacteria | | scientific name |
1239 | Firmicutes | | scientific name |
2157 | Archaea | | scientific name |
2323 | unclassified Bacteria | | scientific name |
13373 | Burkholderia mallei | | scientific name |
28211 | Alphaproteobacteria | | scientific name |
28216 | Betaproteobacteria | | scientific name |
31989 | Rhodobacteraceae | | scientific name |
32008 | Burkholderia | | scientific name |
33807 | unclassified Alphaproteobacteria (miscellaneous) | | scientific name |
33811 | unclassified Gammaproteobacteria (miscellaneous) | | scientific name |
39779 | unclassified Clostridiales (miscellaneous) | | scientific name |
41294 | Bradyrhizobiaceae | | scientific name |
41297 | Sphingomonadaceae | | scientific name |
46255 | Weissella | | scientific name |
47928 | environmental samples | environmental samples <clostridial firmicutes> | scientific name |
48510 | environmental samples | environmental samples <Archaea> | scientific name |
80840 | Burkholderiales | | scientific name |
81850 | Leuconostocaceae | | scientific name |
82117 | unclassified Alphaproteobacteria | | scientific name |
91061 | Bacilli | | scientific name |
95818 | Candidatus Saccharibacteria | | scientific name |
111527 | pseudomallei group | | scientific name |
118884 | unclassified Gammaproteobacteria | | scientific name |
119060 | Burkholderiaceae | | scientific name |
131567 | cellular organisms | | scientific name |
165096 | Weissella koreensis | | scientific name |
165697 | Sphingopyxis | | scientific name |
186801 | Clostridia | | scientific name |
186802 | Clostridiales | | scientific name |
186803 | Lachnospiraceae | | scientific name |
186813 | unclassified Clostridiales | | scientific name |
186826 | Lactobacillales | | scientific name |
186928 | unclassified Lachnospiraceae | | scientific name |
204455 | Rhodobacterales | | scientific name |
204457 | Sphingomonadales | | scientific name |
245012 | butyrate-producing bacterium SM4/1 | | scientific name |
349101 | Rhodobacter sphaeroides ATCC 17029 | | scientific name |
370895 | Burkholderia mallei 2002721280 | | scientific name |
434085 | gamma proteobacterium IMCC2047 | | scientific name |
742723 | Lachnospiraceae bacterium 2_1_46FAA | | scientific name |
939301 | alpha proteobacterium SCGC AAA015-O19 | | scientific name |
1009708 | alpha proteobacterium SCGC AAA536-G10 | | scientific name |
1045854 | Weissella koreensis KACC 15510 | | scientific name |
1174684 | Sphingopyxis sp. MC1 | | scientific name |
1229484 | alpha proteobacterium LLX12A | | scientific name |
1230476 | Bradyrhizobium sp. DFCI-1 | | scientific name |
1235799 | Lachnospiraceae bacterium 3-2 | | scientific name |
1263006 | Firmicutes bacterium CAG:170 | | scientific name |
1394711 | Candidatus Saccharibacteria bacterium RAAC3_TM7_1 | | scientific name |
1412874 | uncultured archaeon A07HR60 | | scientific name |
58 changes: 58 additions & 0 deletions biobox_cli/verification/data/taxonomic_binning/taxonomy/nodes.dmp
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1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | |
356 | 28211 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
374 | 41294 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1060 | 31989 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1063 | 1060 | species | RS | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1239 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
2157 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | |
2323 | 2 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
13373 | 111527 | species | BM | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
28211 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
28216 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
31989 | 204455 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
32008 | 119060 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
33807 | 82117 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
33811 | 118884 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
39779 | 186813 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
41294 | 356 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
41297 | 204457 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
46255 | 81850 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
47928 | 1239 | no rank | | 11 | 0 | 11 | 1 | 0 | 1 | 0 | 0 | uncultured |
48510 | 2157 | no rank | | 11 | 0 | 11 | 1 | 0 | 1 | 0 | 0 | uncultured |
80840 | 28216 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
81850 | 186826 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
82117 | 28211 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
91061 | 1239 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
95818 | 2323 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
111527 | 32008 | species group | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
118884 | 1236 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
119060 | 80840 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | |
165096 | 46255 | species | WK | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
165697 | 41297 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
186801 | 1239 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
186802 | 186801 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
186803 | 186802 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
186813 | 186802 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
186826 | 91061 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
186928 | 186803 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
204455 | 28211 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
204457 | 28211 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
245012 | 39779 | species | BB | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
349101 | 1063 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
370895 | 13373 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
434085 | 33811 | species | GP | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
742723 | 186928 | species | LB | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
939301 | 33807 | species | AP | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1009708 | 33807 | species | AP | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1045854 | 165096 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1174684 | 165697 | species | SS | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1229484 | 33807 | species | AP | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1230476 | 374 | species | BS | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1235799 | 186928 | species | LB | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1263006 | 47928 | species | FB | 11 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | uncultured |
1394711 | 95818 | species | CS | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
1412874 | 48510 | species | UA | 11 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | uncultured |

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