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adding auto-annotate and inventory compilation scripts, plus new annotation files #52

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Jan 12, 2017
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adding auto-annotate and inventory compilation scripts, plus new annotation files #52

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9616c72
adding auto-annotate and inventory compilation scripts, plus new anno…
nbokulich Dec 9, 2016
36fee84
updated auto-annotate code
nbokulich Jan 11, 2017
ca2135c
updated integrity tests
nbokulich Jan 11, 2017
b8ce872
updated example dir structure
nbokulich Jan 11, 2017
e1f87d4
updated integrity checks
nbokulich Jan 11, 2017
46343b5
cleaning up old data files
nbokulich Jan 11, 2017
cde399c
cleaning up old files
nbokulich Jan 11, 2017
862b778
inventory compiler
nbokulich Jan 11, 2017
20b176c
modifying directory path names
nbokulich Jan 12, 2017
6cffa9b
fix example file dir name
nbokulich Jan 12, 2017
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -66,3 +66,5 @@ target/

# other
*~

.DS_store
0 .../greengenes/13_8/database-identifiers.tsv → ...nes/13_8/97-otus/database-identifiers.tsv
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0 ...e-1/greengenes/13_8/expected-taxonomy.tsv → ...ngenes/13_8/97-otus/expected-taxonomy.tsv
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32 changes: 32 additions & 0 deletions data/mock-1/greengenes/13-8/97-otus/database-identifiers.tsv
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37 changes: 37 additions & 0 deletions data/mock-1/greengenes/13-8/97-otus/expected-taxonomy.tsv
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Taxonomy MockHiSeq.even
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Clostridium; s__hathewayi 0.0208333333
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__[Eubacterium]; s__biforme 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Proteus; s__ 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides; s__ 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae; g__Alistipes; s__indistinctus 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus 0.0208333334
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__bifidum 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium; s__prausnitzii 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Roseburia; s__ 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Clostridium; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__formicigenerans 0.0208333333
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__[Eubacterium]; s__ 0.0416666667
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis 0.0208333333
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__coli 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.0208333333
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__ 0.0208333333
k__Bacteria; p__Verrucomicrobia; c__Verrucomicrobiae; o__Verrucomicrobiales; f__Verrucomicrobiaceae; g__Akkermansia; s__muciniphila 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Anaerotruncus; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Clostridium; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__torques 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Edwardsiella; s__ 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__ 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Enterobacter; s__cancerogenus 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Clostridium; s__ 0.0624999999
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ 0.0208333334
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__eggerthii 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ovatus 0.0208333333
k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Collinsella; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Coprococcus; s__ 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.1874999997
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__ 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__ 0.0416666666
32 changes: 32 additions & 0 deletions data/mock-1/greengenes/13-8/99-otus/database-identifiers.tsv
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36 changes: 36 additions & 0 deletions data/mock-1/greengenes/13-8/99-otus/expected-taxonomy.tsv
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Taxonomy MockHiSeq.even
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__longicatena 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Ruminococcus; s__lactaris 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__ 0.0208333334
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__eggerthii 0.0208333333
k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Collinsella; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__[Eubacterium]; s__ 0.0416666667
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Proteus; s__ 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__formicigenerans 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Coprococcus; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Clostridium; s__hathewayi 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.0208333333
k__Bacteria; p__Verrucomicrobia; c__Verrucomicrobiae; o__Verrucomicrobiales; f__Verrucomicrobiaceae; g__Akkermansia; s__muciniphila 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Subdoligranulum; s__variabile 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Anaerotruncus; s__ 0.0208333333
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__coli 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__ 0.0416666666
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__[Eubacterium]; s__biforme 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Clostridium; s__ 0.0208333333
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Enterobacter; s__cancerogenus 0.0208333334
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.0208333334
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae; g__Alistipes; s__indistinctus 0.0208333333
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ 0.0208333334
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Roseburia; s__ 0.0208333334
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__bifidum 0.0208333333
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Clostridium; s__ 0.0833333332
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium; s__prausnitzii 0.0208333334
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__torques 0.0208333334
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Edwardsiella; s__ 0.0208333334
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides; s__ 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis 0.0208333333
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.1874999997
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ovatus 0.0208333333
31 changes: 0 additions & 31 deletions data/mock-1/greengenes/13_8/expected-taxonomy.tsv
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21 changes: 21 additions & 0 deletions data/mock-1/silva/123/97-otus/database-identifiers.tsv
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D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Bifidobacteriales;D_4__Bifidobacteriaceae;D_5__Bifidobacterium;D_6__Bifidobacterium pseudocatenulatum KJ803954.1.1386 KC160492.1.1392 JQ805696.1.1454
D_0__Bacteria;D_1__Actinobacteria;D_2__Coriobacteriia;D_3__Coriobacteriales;D_4__Coriobacteriaceae;D_5__Collinsella;D_6__Collinsella intestinalis KP233383.1.1429
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides finegoldii AB222699.1.1485
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides ovatus GU968168.1.1551 X83952.1.1395
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides thetaiotaomicron JN084203.1.1405
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides uniformis str. 3978 T3 ii JNHN01000175.148172.149576 JNHN01000180.20031.21416
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides vulgatus JN084209.1.1374
D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Bacteroidaceae;D_5__Bacteroides;D_6__Bacteroides xylanisolvens AM230650.1.1368
D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Streptococcaceae;D_5__Streptococcus;D_6__Streptococcus infantarius subsp. infantarius KC699206.1.1387 HQ662525.1.1386 JQ754456.1.1405 KC699128.1.1426
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Clostridiaceae 1;D_5__Clostridium sensu stricto 18;D_6__Clostridium sporogenes DQ680019.1.1418 AY321655.1.1585
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Family XI;D_5__Anaerococcus;D_6__Anaerococcus hydrogenalis D14140.1.1375
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Lachnospiraceae;D_5__Dorea;D_6__Dorea formicigenerans ATCC 27755 AAXA02000007.1.1294
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Lachnospiraceae;D_5__Dorea;D_6__Dorea longicatena AJ132842.30.1345
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Lachnospiraceae;D_5__Lachnoclostridium 5;D_6__[Clostridium] saccharolyticum FJ957875.1.1447 AY604565.1.1311
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Lachnospiraceae;D_5__Tyzzerella 4;D_6__Tyzzerella nexilis DM464569.1.1397
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Ruminococcaceae;D_5__Faecalibacterium;D_6__Faecalibacterium prausnitzii HQ457028.1.1424 JN037416.1.1278
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Ruminococcaceae;D_5__Ruminiclostridium 9;D_6__[Clostridium] leptum HW313913.1.1460 HW313914.1.1485
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Enterobacteriales;D_4__Enterobacteriaceae;D_5__Edwardsiella;D_6__Edwardsiella tarda AF053975.1.1346 KF704685.1.1394 KC884662.1.1426 HQ611038.1.1415 AY775313.1.1414 HM003641.1.1456 JX866954.1.1294 DQ233654.1.1460 EF371905.1.1444
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Enterobacteriales;D_4__Enterobacteriaceae;D_5__Enterobacter;D_6__Enterobacter cancerogenus HQ407289.1.1339 KJ826607.1.1520 HQ407294.1.1349 JN969335.1.1463 FM210031.1.1447 KC834378.1.1334 JQ682639.1.1465 KF817792.1.1394 JX173560.1.1359
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Enterobacteriales;D_4__Enterobacteriaceae;D_5__Escherichia-Shigella;D_6__Escherichia coli LN558634.1.1331 AY776275.1.1463 KF792059.1.1489 KC254646.1.1485 KM504998.1.1406 JJNT01000040.111042.112820 CP007394.148.1706 EF025911.1.1504 HF584703.1.1466 GU594295.1.1477 LM995745.228347.229599 CP009106.160499.162042 HQ219945.1.1457 AB480753.1.1508 KC504012.1.1473 LN558644.1.1476 CP007394.3516165.3517696 LN558643.1.1484 FJ463818.1.1541 HQ857765.1.1444 JN969333.1.1531 GQ273521.1.1399 JSPY01000020.293.1691 GU594318.1.1473 FJ950694.1.1472 KC504010.1.1476 KF500595.1.1479 KC254645.1.1467 CP007393.191798.193312 FJ463821.1.1502 HF584706.1.1465 CCVR01000230.143318.144957 GQ222403.1.1443
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Enterobacteriales;D_4__Enterobacteriaceae;D_5__Providencia;D_6__Providencia alcalifaciens HQ407249.1.1463 KC210832.1.1407
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