lederhosen 0.1.3 → 0.1.4

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Files changed (9) hide show
  1. data/lib/lederhosen/helpers.rb +8 -6
  2. data/lib/version.rb +1 -1
  3. data/spec/data/blast_out.txt +10 -0
  4. data/spec/data/blat.txt +86 -0
  5. data/spec/data/otus.csv +4 -0
  6. data/spec/helpers_spec.rb +2 -2
  7. data/spec/pipeline_spec.rb +14 -2
  8. metadata +10 -5
  9. data/lib/lederhosen/tasks/hierarchical.rb +0 -40
data/lib/lederhosen/helpers.rb CHANGED
@@ -14,7 +14,7 @@ module Lederhosen
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  # Trim a pair of QSEQ files. Saves to a single,
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  # interleaved .fasta file
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  def trim_pairs(left, right, out, args={})
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- cutoff = args[:cutoff] || 20
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+ cutoff = args[:cutoff] || 20
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  min_length = args[:min_length] || 70
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  left_handle = File.open left
@@ -54,10 +54,12 @@ module Lederhosen
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  # throw away any read with an ambiguous primer
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  return nil if dna.sequence =~ /N/
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- min = args[:min] || 20
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+ min = args[:min] || 20
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  offset = args[:cutoff] || 64
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- _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
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- dna.quality.each_byte.each_with_index do |b, a|
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+
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+ _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
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+
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+ dna.quality.each_byte.each_with_index do |b, a|
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  _sum += (b - offset - min)
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  if _sum > _max
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  _max = _sum
@@ -101,7 +103,7 @@ module Lederhosen
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  querylabel = line[8]
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  targetlabel = line[9]
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  sample = line[8].split(':')[2]
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-
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+
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  # keep track of samples
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  samples.add sample
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@@ -127,4 +129,4 @@ module Lederhosen
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  end # class << self
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  end # class Helpers
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- end # Module
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+ end # Module
data/lib/version.rb CHANGED
@@ -1,3 +1,3 @@
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  module Lederhosen
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- VERSION = '0.1.3'
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+ VERSION = '0.1.4'
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  end
data/spec/data/blast_out.txt ADDED
@@ -0,0 +1,10 @@
1
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobacteraceae;[5]Desulfofrigus;[6]Desulfofrigus_sp.;[7]Desulfofrigus_sp._NB81[8]Desulfofrigus_sp._NB81|AJ866935;IVSSEONN 92.98 57 4 0 76 132 527 583 4.7e-21 99.0
2
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]null;[6]bacterium_Ellin6099;[7]bacterium_Ellin6099[8]bacterium_Ellin6099|AY234751;CIOITEJS 100.00 50 0 0 82 131 491 540 4.8e-21 99.0
3
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_IGE-018[8]Acidobacteria_bacterium_IGE-018|GU187039;XNRAMWJO 100.00 50 0 0 82 131 465 514 4.8e-21 99.0
4
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobulbaceae;[5]Desulfurivibrio;[6]Desulfurivibrio_alkaliphilus;[7]Desulfurivibrio_alkaliphilus_AHT2[8]Desulfurivibrio_alkaliphilus_AHT2|CP001940;HBUKOWIN 89.06 64 6 1 89 152 551 613 3.7e-20 96.0
5
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobulbaceae;[5]Desulfurivibrio;[6]Desulfurivibrio_alkaliphilus;[7]Desulfurivibrio_alkaliphilus_AHT2[8]Desulfurivibrio_alkaliphilus_AHT2|CP001940;RIOOMPXJ 89.06 64 6 1 89 152 551 613 3.7e-20 96.0
6
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobulbaceae;[5]Desulfotalea;[6]Desulfotalea_psychrophila;[7]Desulfotalea_psychrophila[8]Desulfotalea_psychrophila_(T)|AF099062;RTWUGGVN 94.55 55 3 0 77 131 530 584 4.7e-20 96.0
7
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobulbaceae;[5]Desulfotalea;[6]Desulfotalea_psychrophila;[7]Desulfotalea_psychrophila_LSv54[8]Desulfotalea_psychrophila_LSv54|CR522870;FWWHMEPI 94.55 55 3 0 77 131 529 583 4.7e-20 96.0
8
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]null;[6]bacterium_Ellin6075;[7]bacterium_Ellin6075[8]bacterium_Ellin6075|AY234727;FRJWBBIH 98.00 50 1 0 82 131 488 537 1.2e-19 94.0
9
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]null;[6]bacterium_Ellin6075;[7]bacterium_Ellin6075[8]bacterium_Ellin6075|AY234727;FRJWBBIH 94.74 19 1 0 137 155 542 560 1.7e-01 34.0
10
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_IGE-017[8]Acidobacteria_bacterium_IGE-017|GU187032;NNORHHJC 98.00 50 1 0 82 131 469 518 1.2e-19 94.0
data/spec/data/blat.txt ADDED
@@ -0,0 +1,86 @@
1
+ 10233:1:IL3_L_1_B_092:cluster-183 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]null;[5]Enhygromyxa;[6]Enhygromyxa_salina;[7]Enhygromyxa_salina[8]Enhygromyxa_salina|HM769728;SBFAJONJ 97.50 80 2 0 76 155 549 628 1.2e-36 151.0
2
+ 10481:1:IL3_L_1_B_125:cluster-172 [0]Bacteria;[1]Bacteroidetes;[2]null;[3]null;[4]null;[5]null;[6]Bacteroidetes_bacterium;[7]Bacteroidetes_bacterium_ONC2[8]Bacteroidetes_bacterium_ONC2|FN554386;BNOVTMLP 93.75 80 5 0 76 155 303 382 7.3e-33 138.0
3
+ 105398:1:IL3_L_1_B_116:cluster-33 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]null;[4]null;[5]null;[6]actinobacterium_YJF1-30;[7]actinobacterium_YJF1-30[8]actinobacterium_YJF1-30|FJ405885;BOXORDKU 96.25 80 3 0 77 156 526 605 1.7e-34 144.0
4
+ 10637:1:IL3_L_1_B_116:cluster-59 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]null;[4]null;[5]null;[6]Rubrobacteridae_bacterium;[7]Rubrobacteridae_bacterium_F2-223[8]Rubrobacteridae_bacterium_F2-223|JF423906;ADNQWEXL 92.41 79 6 0 77 155 529 607 3.4e-31 133.0
5
+ 1155:1:IL3_L_1_B_079:cluster-260 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rickettsiales;[4]Anaplasmataceae;[5]Wolbachia;[6]Candidatus_Wolbachia;[7]Candidatus_Wolbachia_inokumae[8]Candidatus_Wolbachia_inokumae|DQ402518;BHHLGMCD 95.92 49 2 0 79 127 472 520 9.8e-18 88.0
6
+ 119671:1:IL3_L_1_B_108:cluster-510 [0]Bacteria;[1]Verrucomicrobia;[2]Verrucomicrobiae;[3]Verrucomicrobiales;[4]Verrucomicrobiaceae;[5]Haloferula;[6]Haloferula_phyci;[7]Haloferula_phyci[8]Haloferula_phyci_(T)|AB372854;IQEDJXXG 88.06 67 8 0 86 152 526 592 1.9e-21 100.0
7
+ 121837:1:IL3_L_1_B_108:cluster-85 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]alpha_proteobacterium;[7]alpha_proteobacterium_CN37[8]alpha_proteobacterium_CN37|FN554393;UVHJKDIU 97.47 79 2 0 78 156 444 522 7.1e-36 148.0
8
+ 12285:1:IL3_L_1_B_120:cluster-86 [0]Bacteria;[1]Bacteroidetes;[2]Bacteroidia;[3]Bacteroidales;[4]Porphyromonadaceae;[5]null;[6]Porphyromonadaceae_bacterium;[7]Porphyromonadaceae_bacterium_NML_060648[8]Porphyromonadaceae_bacterium_NML_060648|EF184292;QCALEPTL 93.51 77 5 0 77 153 491 567 4.3e-32 136.0
9
+ 12437:1:IL3_L_1_B_100:cluster-286 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobacteraceae;[5]Desulfofrigus;[6]Desulfofrigus_sp.;[7]Desulfofrigus_sp._NB81[8]Desulfofrigus_sp._NB81|AJ866935;IVSSEONN 87.01 77 10 0 75 151 527 603 6.2e-26 115.0
10
+ 12516:1:IL3_L_1_B_110:cluster-356 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhodospirillales;[4]Acetobacteraceae;[5]Acidisphaera;[6]Acidisphaera_sp.;[7]Acidisphaera_sp._NO-15[8]Acidisphaera_sp._NO-15|AF376024;DVMCNHFW 97.50 80 2 0 74 153 452 531 4.1e-37 152.0
11
+ 126650:1:IL3_L_1_B_113:cluster-70 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]Acidobacterium;[6]Acidobacterium_sp.;[7]Acidobacterium_sp._ORAC[8]Acidobacterium_sp._ORAC|FN689719;LUXCSWVV 85.90 78 11 0 78 155 456 533 2.6e-26 117.0
12
+ 127079:1:IL3_L_1_B_104:cluster-375 [0]Bacteria;[1]Spirochaetes;[2]Spirochaetes_(class);[3]Spirochaetales;[4]Spirochaetaceae;[5]Spirochaeta;[6]Spirochaeta_sp.;[7]Spirochaeta_sp.[8]Spirochaeta_sp.|M71240;SVITBYOL 91.04 67 6 0 83 149 570 636 9.7e-27 118.0
13
+ 12846:1:IL3_L_1_B_125:cluster-452 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]null;[5]null;[6]myxobacterium_AT3-01;[7]myxobacterium_AT3-01[8]myxobacterium_AT3-01|AB246772;VNFLROYL 94.94 79 4 0 75 153 256 334 1.1e-33 141.0
14
+ 142709:1:IL3_L_1_B_113:cluster-352 [0]Bacteria;[1]Firmicutes;[2]Bacilli;[3]Bacillales;[4]null;[5]null;[6]Bacillales_bacterium;[7]Bacillales_bacterium_Gsoil_1105[8]Bacillales_bacterium_Gsoil_1105|AB245375;AURFXFIN 97.30 74 2 0 74 147 520 593 2.4e-33 140.0
15
+ 154017:1:IL3_L_1_B_113:cluster-153 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhizobiales;[4]Hyphomicrobiaceae;[5]Hyphomicrobium;[6]Hyphomicrobium_sp.;[7]Hyphomicrobium_sp._WG6[8]Hyphomicrobium_sp._WG6|AY934488;TFFCIKFL 92.00 75 6 0 76 150 433 507 6.7e-29 125.0
16
+ 161430:1:IL3_L_1_B_113:cluster-628 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]Xanthomonadales;[4]Xanthomonadaceae;[5]Stenotrophomonas;[6]Stenotrophomonas_maltophilia;[7]Stenotrophomonas_maltophilia[8]Stenotrophomonas_maltophilia|AY277550;BNXRNYFN 88.89 72 8 0 72 143 470 541 2.6e-24 110.0
17
+ 164650:1:IL3_L_1_B_112:cluster-269 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]Haliangiaceae;[5]Haliangium;[6]Haliangium_ochraceum;[7]Haliangium_ochraceum[8]Haliangium_ochraceum|EF108312;YBKPFGCT 91.55 71 6 0 81 151 548 618 5.9e-27 119.0
18
+ 16523:1:IL3_L_1_B_111:cluster-256 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]null;[4]null;[5]null;[6]Rubrobacteridae_bacterium;[7]Rubrobacteridae_bacterium_F2-223[8]Rubrobacteridae_bacterium_F2-223|JF423906;ADNQWEXL 97.47 79 2 0 76 154 529 607 8.3e-36 148.0
19
+ 165493:1:IL3_L_1_B_113:cluster-374 [0]Bacteria;[1]Bacteroidetes;[2]Sphingobacteria;[3]Sphingobacteriales;[4]null;[5]Flavisolibacter;[6]Flavosolibacter_sp.;[7]Flavosolibacter_sp._HU1-JC5[8]Flavosolibacter_sp._HU1-JC5|FJ177533;BQOMHIKW 98.75 80 1 0 74 153 435 514 3.5e-37 153.0
20
+ 166424:1:IL3_L_1_B_112:cluster-201 [0]Bacteria;[1]Proteobacteria;[2]Epsilonproteobacteria;[3]null;[4]null;[5]null;[6]epsilon_proteobacterium;[7]epsilon_proteobacterium_B155-1[8]epsilon_proteobacterium_B155-1|AB175506;WNIFAJRW 96.23 53 2 0 77 129 505 557 1.0e-20 98.0
21
+ 16707:1:IL3_L_1_B_136:cluster-810 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]null;[5]Enhygromyxa;[6]Enhygromyxa_salina;[7]Enhygromyxa_salina[8]Enhygromyxa_salina|HM769729;PJERVOLW 93.10 58 4 0 71 128 517 574 1.3e-21 101.0
22
+ 1693:1:IL3_L_1_B_100:cluster-326 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Syntrophobacterales;[4]Syntrophaceae;[5]Syntrophus;[6]Syntrophus_sp.;[7]Syntrophus_sp.[8]Syntrophus_sp.|AJ133794;FSITSDQN 82.67 75 13 0 75 149 541 615 3.1e-23 106.0
23
+ 173144:1:IL3_L_1_B_112:cluster-166 [0]Bacteria;[1]Bacteroidetes;[2]Sphingobacteria;[3]Sphingobacteriales;[4]Sphingobacteriaceae;[5]Sphingobacterium;[6]Sphingobacterium_composti;[7]Sphingobacterium_composti_Yoo_et_al._2007[8]Sphingobacterium_composti_Yoo_et_al._2007|EF122436;FWRIYPUO 94.92 59 3 0 76 134 510 568 2.8e-23 106.0
24
+ 173264:1:IL3_L_1_B_113:cluster-303 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhizobiales;[4]Hyphomicrobiaceae;[5]Blastochloris;[6]Blastochloris_sp.;[7]Blastochloris_sp._TUT3225[8]Blastochloris_sp._TUT3225|AB250618;FHBRMKDV 94.03 67 4 0 88 154 483 549 7.3e-28 122.0
25
+ 17528:1:IL3_L_1_B_123:cluster-46 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]Acidopila;[6]Acidopila_rosea;[7]Acidopila_rosea[8]Acidopila_rosea|AB561884;WWBGOAHV 96.25 80 3 0 77 156 484 563 1.5e-35 147.0
26
+ 18443:1:IL3_L_1_B_081:cluster-38 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]Actinomycetales;[4]Nocardioidaceae;[5]Nocardioides;[6]Nocardioides_sp.;[7]Nocardioides_sp._ND6[8]Nocardioides_sp._ND6|AJ511294;DTWLXVKU 100.00 80 0 0 77 156 520 599 1.1e-38 158.0
27
+ 19567:1:IL3_L_1_B_128:cluster-79 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]Cystobacteraceae;[5]Cystobacter;[6]Cystobacter_sp.;[7]Cystobacter_sp._94032[8]Cystobacter_sp._94032|DQ520899;QSSQAFOU 96.20 79 3 0 78 156 532 610 3.3e-34 143.0
28
+ 2134:1:IL3_L_1_B_136:cluster-218 [0]Bacteria;[1]Firmicutes;[2]Bacilli;[3]Lactobacillales;[4]Lactobacillaceae;[5]Lactobacillus;[6]Lactobacillus_sp.;[7]Lactobacillus_sp._61D[8]Lactobacillus_sp._61D|FR681902;QMMLDAFV 88.31 77 9 0 76 152 153 77 3.7e-27 119.0
29
+ 21459:1:IL3_L_1_B_091:cluster-31 [0]Bacteria;[1]Acidobacteria;[2]Holophagae;[3]Holophagales;[4]Holophagaceae;[5]Holophaga;[6]Holophaga_foetida;[7]Holophaga_foetida[8]Holophaga_foetida_(T)|X77215;UUQYFQKU 97.50 80 2 0 77 156 522 601 2.2e-36 150.0
30
+ 21891:1:IL3_L_1_B_125:cluster-83 [0]Bacteria;[1]Bacteroidetes;[2]Sphingobacteria;[3]Sphingobacteriales;[4]Saprospiraceae;[5]Haliscomenobacter;[6]Candidatus_Haliscomenobacter;[7]Candidatus_Haliscomenobacter_calcifugiens[8]Candidatus_Haliscomenobacter_calcifugiens|AJ786327;TQWDQCFL 96.10 77 3 0 77 153 497 573 2.9e-33 140.0
31
+ 22276:1:IL3_L_1_B_113:cluster-337 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]alpha_proteobacterium;[7]alpha_proteobacterium_KC-IT-H9[8]alpha_proteobacterium_KC-IT-H9|FJ711207;NBTKISNO 94.55 55 3 0 75 129 470 524 3.1e-20 96.0
32
+ 2262:1:IL3_L_1_B_128:cluster-283 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]null;[4]null;[5]null;[6]bacterium_Ellin5082;[7]bacterium_Ellin5082[8]bacterium_Ellin5082|AY234499;KVRDSHPW 97.47 79 2 0 75 153 431 509 1.2e-36 151.0
33
+ 26810:1:IL3_L_1_B_136:cluster-180 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]null;[4]null;[5]null;[6]gamma_proteobacterium;[7]gamma_proteobacterium_ectosymbiont_of_Rimicaris_exoculata[8]gamma_proteobacterium_ectosymbiont_of_Rimicaris_exoculata|FM203388;NHOTUMPA 91.36 81 6 1 76 155 507 587 6.9e-29 125.0
34
+ 27553:1:IL3_L_1_B_115:cluster-112 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]null;[5]null;[6]Clostridiales_bacterium;[7]Clostridiales_bacterium_10-3b[8]Clostridiales_bacterium_10-3b|HQ452860;PMIGQOJQ 93.75 64 4 0 78 141 528 591 2.2e-25 113.0
35
+ 27667:1:IL3_L_1_B_110:cluster-259 [0]Bacteria;[1]Bacteroidetes;[2]Sphingobacteria;[3]Sphingobacteriales;[4]Sphingobacteriaceae;[5]Mucilaginibacter;[6]Mucilaginibacter_daejeonensis;[7]Mucilaginibacter_daejeonensis[8]Mucilaginibacter_daejeonensis_(T)|AB267717;MWJAPLHJ 97.47 79 2 0 76 154 509 587 2.3e-35 147.0
36
+ 27704:1:IL3_L_1_B_072:cluster-6 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhizobiales;[4]Bradyrhizobiaceae;[5]Bosea;[6]Bosea_thiooxidans;[7]Bosea_thiooxidans[8]Bosea_thiooxidans|AF508112;USJPDGDE 90.91 66 6 0 91 156 475 540 4.0e-23 106.0
37
+ 28622:1:IL3_L_1_B_079:cluster-48 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]bacterium_Ellin5086;[7]bacterium_Ellin5086[8]bacterium_Ellin5086|AY234503;LFEHRVJR 96.20 79 3 0 77 155 450 528 2.4e-35 146.0
38
+ 29556:1:IL3_L_1_B_115:cluster-394 [0]Bacteria;[1]Bacteroidetes;[2]Flavobacteria;[3]Flavobacteriales;[4]Flavobacteriaceae;[5]Aequorivita;[6]Aequorivita_capsosiphonis;[7]Aequorivita_capsosiphonis[8]Aequorivita_capsosiphonis_(T)|EU290153;SLXGGEAU 97.50 80 2 0 74 153 486 565 1.4e-36 151.0
39
+ 3075:1:IL3_L_1_B_132:cluster-45 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_KBS_96[8]Acidobacteria_bacterium_KBS_96|FJ870384;QSXTJUMD 93.75 80 5 0 77 156 460 539 5.9e-34 142.0
40
+ 30861:1:IL3_L_1_B_131:cluster-163 [0]Bacteria;[1]Acidobacteria;[2]Acidobacteria_(class);[3]Acidobacteriales;[4]Acidobacteriaceae;[5]null;[6]bacterium_Ellin5121;[7]bacterium_Ellin5121[8]bacterium_Ellin5121|AY234538;BPVMNCIT 93.67 79 5 0 77 155 471 549 3.1e-34 143.0
41
+ 31620:1:IL3_L_1_B_131:cluster-28 [0]Bacteria;[1]Bacteroidetes;[2]Bacteroidia;[3]Bacteroidales;[4]Bacteroidaceae;[5]Bacteroides;[6]Bacteroides_clarus;[7]Bacteroides_clarus[8]Bacteroides_clarus|AB547638;PAVSUDNR 100.00 80 0 0 77 156 526 605 3.1e-38 156.0
42
+ 34415:1:IL3_L_1_B_116:cluster-350 [0]Bacteria;[1]Gemmatimonadetes;[2]Gemmatimonadetes_(class);[3]Gemmatimonadales;[4]Gemmatimonadaceae;[5]Gemmatimonas;[6]Gemmatimonas_aurantiaca;[7]Gemmatimonas_aurantiaca_T-27[8]Gemmatimonas_aurantiaca_T-27|AP009153;WYQEUNQH 96.88 64 2 0 74 137 514 577 7.5e-28 122.0
43
+ 3611:1:IL3_L_1_B_113:cluster-479 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]Xanthomonadales;[4]Sinobacteraceae;[5]Steroidobacter;[6]Steroidobacter_sp.;[7]Steroidobacter_sp._ZUMI_37[8]Steroidobacter_sp._ZUMI_37|AB548216;XEYEQEIX 98.44 64 1 0 76 139 531 594 2.2e-28 123.0
44
+ 36358:1:IL3_L_1_B_094:cluster-550 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]alpha_proteobacterium;[7]alpha_proteobacterium_ACD1[8]alpha_proteobacterium_ACD1|AY965893;OCKRXHRM 93.75 64 4 0 73 136 396 459 1.2e-24 111.0
45
+ 3799:1:IL3_L_1_B_117:cluster-216 [0]Bacteria;[1]Bacteroidetes;[2]null;[3]null;[4]null;[5]null;[6]Bacteroidetes_bacterium;[7]Bacteroidetes_bacterium_GS[8]Bacteroidetes_bacterium_GS|AB539998;UISTEOXY 96.20 79 3 0 75 153 448 526 2.5e-34 143.0
46
+ 39361:1:IL3_L_1_B_094:cluster-62 [0]Bacteria;[1]Verrucomicrobia;[2]Spartobacteria;[3]null;[4]null;[5]null;[6]bacterium_Ellin507;[7]bacterium_Ellin507[8]bacterium_Ellin507|AY960770;RTOUTNEC 96.20 79 3 0 78 156 517 595 4.7e-35 146.0
47
+ 40837:1:IL3_L_1_B_106:cluster-136 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]Ruminococcaceae;[5]Ruminococcus;[6]Ruminococcus_sp.;[7]Ruminococcus_sp._NML_00-0124[8]Ruminococcus_sp._NML_00-0124|EU815223;ARPTISJA 97.40 77 2 0 76 152 459 535 3.3e-35 146.0
48
+ 41412:1:IL3_L_1_B_113:cluster-328 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhizobiales;[4]Beijerinckiaceae;[5]Chelatococcus;[6]Chelatococcus_sp.;[7]Chelatococcus_sp._P-117[8]Chelatococcus_sp._P-117|AM412118;DBOTGAMI 93.67 79 5 0 75 153 451 529 2.2e-33 140.0
49
+ 42373:1:IL3_L_1_B_106:cluster-176 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]Acidimicrobiales;[4]Iamiaceae;[5]Iamia;[6]Iamia_sp.;[7]Iamia_sp._T2-YC6790[8]Iamia_sp._T2-YC6790|GQ369058;XRJMDLFX 97.47 79 2 0 77 155 515 593 2.5e-36 150.0
50
+ 42508:1:IL3_L_1_B_106:cluster-575 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhodobacterales;[4]Rhodobacteraceae;[5]Maribius;[6]Maribius_sp.;[7]Maribius_sp._Y26[8]Maribius_sp._Y26|FJ230842;HVKAFVCU 92.11 76 6 0 73 148 435 510 8.3e-30 128.0
51
+ 42606:1:IL3_L_1_B_072:cluster-50 [0]Bacteria;[1]Firmicutes;[2]Bacilli;[3]Lactobacillales;[4]Lactobacillaceae;[5]Lactobacillus;[6]Lactobacillus_sp.;[7]Lactobacillus_sp._66c[8]Lactobacillus_sp._66c|FR681900;QQPLXBXK 93.75 48 1 1 78 123 145 98 6.2e-15 79.0
52
+ 42742:1:IL3_L_1_B_094:cluster-313 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]bacterium_Ellin6089;[7]bacterium_Ellin6089[8]bacterium_Ellin6089|AY234741;DCERQPKI 96.25 80 3 0 74 153 460 539 1.4e-35 147.0
53
+ 45955:1:IL3_L_1_B_094:cluster-74 [0]Bacteria;[1]Chlamydiae;[2]Chlamydiae_(class);[3]Chlamydiales;[4]null;[5]null;[6]Chlamydiales_bacterium;[7]Chlamydiales_bacterium_CRIB33[8]Chlamydiales_bacterium_CRIB33|EU683887;HLCLAHGH 97.40 77 2 0 77 153 453 529 2.4e-34 143.0
54
+ 4910:1:IL3_L_1_B_076:cluster-1 [0]Bacteria;[1]Verrucomicrobia;[2]null;[3]null;[4]null;[5]null;[6]Verrucomicrobia_bacterium;[7]Verrucomicrobia_bacterium_OR-59[8]Verrucomicrobia_bacterium_OR-59|HM163278;GTOSOCHD 98.73 79 1 0 78 156 510 588 3.9e-37 152.0
55
+ 493:1:IL3_L_1_B_131:cluster-380 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]Lachnospiraceae;[5]null;[6]Lachnospiraceae_bacterium;[7]Lachnospiraceae_bacterium_28-4[8]Lachnospiraceae_bacterium_28-4|DQ789121;IQRDAQKE 97.50 80 2 0 74 153 513 592 3.2e-37 153.0
56
+ 50627:1:IL3_L_1_B_132:cluster-363 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_Ellin7137[8]Acidobacteria_bacterium_Ellin7137|AY673303;SVKAXTOO 80.26 76 15 0 74 149 480 555 4.6e-19 92.0
57
+ 51610:1:IL3_L_1_B_125:cluster-69 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]Polyangiaceae;[5]Sorangium;[6]Sorangium_cellulosum;[7]Sorangium_cellulosum[8]Sorangium_cellulosum|EU240531;CFOVMDMI 94.55 55 3 0 78 132 510 564 7.3e-21 98.0
58
+ 56408:1:IL3_L_1_B_132:cluster-0 [0]Bacteria;[1]Nitrospirae;[2]Nitrospira_(class);[3]Nitrospirales;[4]Nitrospiraceae;[5]Nitrospira;[6]Nitrospira_sp.;[7]Nitrospira_sp.[8]Nitrospira_sp.|AJ224042;FIKWHBDQ 94.94 79 4 0 77 155 521 599 7.4e-34 142.0
59
+ 56623:1:IL3_L_1_B_106:cluster-139 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]Clostridiaceae;[5]Clostridium;[6]Clostridium_isatidis;[7]Clostridium_isatidis[8]Clostridium_isatidis_(T)|X98395;UOUGWHSK 98.75 80 1 0 76 155 468 547 3.9e-37 152.0
60
+ 57129:1:IL3_L_1_B_113:cluster-388 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]Pseudomonadales;[4]Moraxellaceae;[5]Acinetobacter;[6]Acinetobacter_sp.;[7]Acinetobacter_sp._HY-7[8]Acinetobacter_sp._HY-7|EU580737;VHVBCRQR 85.90 78 11 0 75 152 527 604 7.2e-25 112.0
61
+ 62372:1:IL3_L_1_B_091:cluster-910 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]null;[4]null;[5]null;[6]actinobacterium_TC4;[7]actinobacterium_TC4[8]actinobacterium_TC4|JF510471;GXSLEYNY 95.18 83 4 0 68 150 457 539 1.0e-36 151.0
62
+ 6417:1:IL3_L_1_B_072:cluster-192 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Desulfobacterales;[4]Desulfobacteraceae;[5]Desulfofrigus;[6]Desulfofrigus_sp.;[7]Desulfofrigus_sp._NB81[8]Desulfofrigus_sp._NB81|AJ866935;IVSSEONN 92.98 57 4 0 76 132 527 583 4.7e-21 99.0
63
+ 67120:1:IL3_L_1_B_104:cluster-370 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_IGE-011[8]Acidobacteria_bacterium_IGE-011|GU187027;UDHRJGIW 96.10 77 3 0 75 151 483 559 5.4e-34 142.0
64
+ 67673:1:IL3_L_1_B_125:cluster-727 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]Myxococcaceae;[5]Myxococcus;[6]Myxococcus_fulvus;[7]Myxococcus_fulvus[8]Myxococcus_fulvus|EU262996;NLQYFNUS 88.57 70 8 0 81 150 551 620 1.2e-24 111.0
65
+ 7276:1:IL3_L_1_B_104:cluster-656 [0]Bacteria;[1]Proteobacteria;[2]Betaproteobacteria;[3]Burkholderiales;[4]Comamonadaceae;[5]Variovorax;[6]Variovorax_paradoxus;[7]Variovorax_paradoxus[8]Variovorax_paradoxus|AY169431;HCDSTDDB 100.00 80 0 0 72 151 520 599 1.9e-38 157.0
66
+ 7351:1:IL3_L_1_B_113:cluster-251 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Rhodospirillales;[4]Rhodospirillaceae;[5]Marispirillum;[6]Marispirillum_indicum;[7]Marispirillum_indicum[8]Marispirillum_indicum_(T)|EU642410;WFHBJRJX 95.00 80 4 0 75 154 469 548 1.8e-34 144.0
67
+ 74004:1:IL3_L_1_B_128:cluster-13 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_IGE-008[8]Acidobacteria_bacterium_IGE-008|GU187025;YPJYKKBR 94.59 74 4 0 83 156 491 564 1.8e-30 130.0
68
+ 74582:1:IL3_L_1_B_116:cluster-11 [0]Bacteria;[1]Planctomycetes;[2]Planctomycetacia;[3]Planctomycetales;[4]Planctomycetaceae;[5]Singulisphaera;[6]Singulisphaera_acidiphila;[7]Singulisphaera_acidiphila[8]Singulisphaera_acidiphila_(T)|AM850678;MCXYMBLX 100.00 79 0 0 78 156 488 566 6.0e-38 155.0
69
+ 77723:1:IL3_L_1_B_113:cluster-502 [0]Bacteria;[1]Bacteroidetes;[2]Sphingobacteria;[3]Sphingobacteriales;[4]null;[5]Chitinophaga;[6]Chitinophaga_pinensis;[7]Chitinophaga_pinensis_DSM_2588[8]Chitinophaga_pinensis_DSM_2588|CP001699;WRBCNFXM 97.50 80 2 0 73 152 527 606 2.0e-36 150.0
70
+ 78138:1:IL3_L_1_B_124:cluster-266 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]Eubacteriaceae;[5]Eubacterium;[6]Eubacterium_sp.;[7]Eubacterium_sp._BBDP67[8]Eubacterium_sp._BBDP67|DQ337532;HQTMQFHA 89.19 74 8 0 75 148 517 590 1.2e-26 118.0
71
+ 7844:1:IL3_L_1_B_138:cluster-35 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Syntrophobacterales;[4]Syntrophobacteraceae;[5]Thermodesulforhabdus;[6]Thermodesulforhabdus_norvegica;[7]Thermodesulforhabdus_norvegica[8]Thermodesulforhabdus_norvegica_(T)|U25627;LHYMMQQX 87.50 80 9 1 77 156 569 647 6.7e-27 118.0
72
+ 7:1:IL3_L_1_B_092:cluster-190 [0]Bacteria;[1]Planctomycetes;[2]Planctomycetacia;[3]Planctomycetales;[4]Planctomycetaceae;[5]Pirellula;[6]Pirellula_sp.;[7]Pirellula_sp.[8]Pirellula_sp.|X81947;JWWUNYIW 91.43 70 6 0 86 155 499 568 1.6e-25 114.0
73
+ 82477:1:IL3_L_1_B_104:cluster-366 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]Myxococcales;[4]Polyangiaceae;[5]Chondromyces;[6]Chondromyces_apiculatus;[7]Chondromyces_apiculatus[8]Chondromyces_apiculatus|AJ233938;MYGBVEQB 98.04 51 1 0 76 126 528 578 1.1e-20 98.0
74
+ 83351:1:IL3_L_1_B_108:cluster-498 [0]Bacteria;[1]Firmicutes;[2]Bacilli;[3]Lactobacillales;[4]null;[5]null;[6]Lactobacillales_bacterium;[7]Lactobacillales_bacterium_HY-36-1[8]Lactobacillales_bacterium_HY-36-1|AY581272;JVTTHISC 92.31 78 6 0 73 150 480 557 1.5e-31 134.0
75
+ 8501:1:IL3_L_1_B_136:cluster-84 [0]Bacteria;[1]Proteobacteria;[2]Deltaproteobacteria;[3]null;[4]null;[5]null;[6]Olavius_crassitunicatus;[7]Olavius_crassitunicatus_delta-proteobacterial_endosymbiont[8]Olavius_crassitunicatus_delta-proteobacterial_endosymbiont|AJ620510;MRBSOCOD 87.50 80 10 0 77 156 546 625 8.1e-29 125.0
76
+ 86955:1:IL3_L_1_B_104:cluster-227 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]Pseudomonadales;[4]Pseudomonadaceae;[5]Pseudomonas;[6]Pseudomonas_sp.;[7]Pseudomonas_sp._W1-1[8]Pseudomonas_sp._W1-1|FJ373023;UXRYTNBQ 93.75 80 5 0 75 154 495 574 2.3e-33 140.0
77
+ 87597:1:IL3_L_1_B_132:cluster-433 [0]Bacteria;[1]Acidobacteria;[2]null;[3]null;[4]null;[5]null;[6]Acidobacteria_bacterium;[7]Acidobacteria_bacterium_Ellin7137[8]Acidobacteria_bacterium_Ellin7137|AY673303;SVKAXTOO 95.52 67 3 0 87 153 493 559 4.8e-28 122.0
78
+ 88392:1:IL3_L_1_B_132:cluster-4 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]Xanthomonadales;[4]Xanthomonadaceae;[5]Dokdonella;[6]Dokdonella_koreensis;[7]Dokdonella_koreensis[8]Dokdonella_koreensis_(T)|AY987368;QWTBVLKO 91.25 80 7 0 77 156 501 580 1.3e-30 131.0
79
+ 88581:1:IL3_L_1_B_113:cluster-149 [0]Bacteria;[1]Verrucomicrobia;[2]Verrucomicrobiae;[3]Verrucomicrobiales;[4]Verrucomicrobia_subdivision_3;[5]null;[6]bacterium_Ellin518;[7]bacterium_Ellin518[8]bacterium_Ellin518|AY960781;MDPTOBBQ 89.87 79 8 0 77 155 524 602 5.8e-29 125.0
80
+ 89244:1:IL3_L_1_B_113:cluster-10 [0]Bacteria;[1]Planctomycetes;[2]Planctomycetacia;[3]Planctomycetales;[4]null;[5]null;[6]Planctomycetales_bacterium;[7]Planctomycetales_bacterium_Ellin6207[8]Planctomycetales_bacterium_Ellin6207|AY673166;OTMNGTFS 88.61 79 9 0 78 156 470 548 3.0e-28 123.0
81
+ 8966:1:IL3_L_1_B_111:cluster-480 [0]Bacteria;[1]Firmicutes;[2]Clostridia;[3]Clostridiales;[4]Clostridiaceae;[5]Clostridium;[6]Clostridium_saccharolyticum;[7]Clostridium_saccharolyticum[8]Clostridium_saccharolyticum|FJ957873;POQWATTL 90.28 72 7 0 74 145 503 574 7.2e-25 112.0
82
+ 8998:1:IL3_L_1_B_104:cluster-88 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]null;[4]null;[5]null;[6]alpha_proteobacterium;[7]alpha_proteobacterium_7CY[8]alpha_proteobacterium_7CY|AB076083;RAKFJBSE 89.29 56 6 0 78 133 426 481 9.4e-19 91.0
83
+ 90551:1:IL3_L_1_B_113:cluster-9 [0]Bacteria;[1]Proteobacteria;[2]Gammaproteobacteria;[3]null;[4]null;[5]null;[6]bacterium_Ellin5114;[7]bacterium_Ellin5114[8]bacterium_Ellin5114|AY234531;DOLDDAPH 90.00 80 8 0 77 156 503 582 8.6e-32 135.0
84
+ 9101:1:IL3_L_1_B_120:cluster-219 [0]Bacteria;[1]Verrucomicrobia;[2]Verrucomicrobiae;[3]Verrucomicrobiales;[4]null;[5]null;[6]Verrucomicrobiae_bacterium;[7]Verrucomicrobiae_bacterium_pACH90[8]Verrucomicrobiae_bacterium_pACH90|AY297806;ANFYOROK 97.40 77 2 0 76 152 511 587 8.3e-35 145.0
85
+ 91638:1:IL3_L_1_B_104:cluster-243 [0]Bacteria;[1]Proteobacteria;[2]Alphaproteobacteria;[3]Sphingomonadales;[4]Sphingomonadaceae;[5]null;[6]Sphingomonadaceae_bacterium;[7]Sphingomonadaceae_bacterium_Gsoil_359[8]Sphingomonadaceae_bacterium_Gsoil_359|AB245346;RKWSEPHF 100.00 79 0 0 76 154 457 535 4.7e-38 155.0
86
+ 94693:1:IL3_L_1_B_113:cluster-310 [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria_(class);[3]Actinomycetales;[4]Mycobacteriaceae;[5]Mycobacterium;[6]Mycobacterium_confluentis;[7]Mycobacterium_confluentis[8]Mycobacterium_confluentis|X63608;WDOGKUIR 98.73 79 1 0 75 153 384 462 3.9e-37 152.0
data/spec/data/otus.csv ADDED
@@ -0,0 +1,4 @@
1
+ -,cluster-370,cluster-180,cluster-9,cluster-218,cluster-256,cluster-85,cluster-28,cluster-313,cluster-380,cluster-190,cluster-266,cluster-0,cluster-38,cluster-656,cluster-10,cluster-219,cluster-48,cluster-86,cluster-352,cluster-628,cluster-153,cluster-172,cluster-1,cluster-286,cluster-163,cluster-201,cluster-11,cluster-363,cluster-59,cluster-192,cluster-810,cluster-31,cluster-69,cluster-183,cluster-50,cluster-259,cluster-88,cluster-136,cluster-79,cluster-326,cluster-155,cluster-269,cluster-659,cluster-374,cluster-70,cluster-13,cluster-260,cluster-498,cluster-479,cluster-4,cluster-251,cluster-394,cluster-375,cluster-356,cluster-337,cluster-166,cluster-33,cluster-727,cluster-575,cluster-480,cluster-366,cluster-328,cluster-62,cluster-176,cluster-452,cluster-433,cluster-243,cluster-310,cluster-139,cluster-6,cluster-510,cluster-92,cluster-35,cluster-149,cluster-216,cluster-45,cluster-83,cluster-910,cluster-74,cluster-283,cluster-112,cluster-502,cluster-388,cluster-350,cluster-46,cluster-84,cluster-550,cluster-227,cluster-303
2
+ IL3_L_1_B_072,1174,262,1121,112,25,316,19,322,2,71,149,45,926,515,264,110,64,14,118,55,1995,40,404,107,24,199,91,60,885,1021,53,113,232,267,854,21,141,3,886,237,25,192,374,89,895,4356,149,5,281,1306,213,138,558,13,507,183,49,155,208,3,455,104,2823,445,71,282,575,498,38,612,137,300,116,138,367,211,379,74,38,429,95,496,71,217,11,248,90,258,195
3
+ IL3_L_1_B_073,4,2,10,3,1,3,9,10,3,0,1,0,23,4,2,2,7,20,7,3,36,2,4,0,5,4,0,7,17,15,1,1,2,4,4,2,1,6,9,6,3,3,3,4,22,21,2,0,4,18,1,1,7,1,3,3,0,4,1,6,8,0,42,9,3,5,6,9,15,6,1,1,6,3,6,15,4,0,1,5,2,8,0,3,2,2,3,4,2
4
+ IL3_L_1_B_076,479,70,321,47,16,66,29,89,2,35,90,21,414,159,90,34,32,20,38,11,694,14,140,39,6,62,19,36,536,300,33,48,126,108,478,6,73,5,282,132,86,64,151,39,353,1757,46,7,58,437,51,54,232,5,143,67,25,64,94,6,203,31,1046,235,27,96,112,243,20,188,36,155,21,49,95,53,144,41,14,223,31,120,34,68,3,65,12,54,58
data/spec/helpers_spec.rb CHANGED
@@ -2,7 +2,7 @@ require 'spec_helper'
2
2
 
3
3
  describe Lederhosen::Helpers do
4
4
 
5
- let (:groups) { Lederhosen::Helpers.get_grouped_qseq_files('spec/data/*.txt') }
5
+ let (:groups) { Lederhosen::Helpers.get_grouped_qseq_files('spec/data/IL*.txt') }
6
6
 
7
7
  it 'should have a method for grouping QSEQ files' do
8
8
  groups.length.should == 2
@@ -23,4 +23,4 @@ describe Lederhosen::Helpers do
23
23
  # this test will break if trim parameters change
24
24
  File.read('/tmp/munchen_trim_test.fasta').grep(/^>/).length.should be_even
25
25
  end
26
- end
26
+ end
data/spec/pipeline_spec.rb CHANGED
@@ -10,7 +10,7 @@ describe 'the pipeline' do
10
10
  end
11
11
 
12
12
  it 'should trim reads' do
13
- `./bin/lederhosen trim --reads-dir=spec/data/*.txt --out-dir=#{test_dir}/trimmed`
13
+ `./bin/lederhosen trim --reads-dir=spec/data/IL*.txt --out-dir=#{test_dir}/trimmed`
14
14
  $?.success?.should be_true
15
15
  end
16
16
 
@@ -38,4 +38,16 @@ describe 'the pipeline' do
38
38
  `./bin/lederhosen split --reads=#{test_dir}/joined.fasta --clusters=#{test_dir}/clusters.uc --out-dir=#{test_dir}/split --min-clst-size=1`
39
39
  end
40
40
 
41
- end
41
+ it 'should name clusters given a taxcollector database'
42
+
43
+ it 'should add names to otu abundance matrix given blat output' do
44
+ level = %w{kingdom domain phylum class order genus speces}.choice
45
+ `./bin/lederhosen add_names --table=spec/data/otus.csv --blat=spec/data/blat.txt --level=#{level} --output=#{test_dir}/named_otus.csv`
46
+ $?.success?.should be_true
47
+ end
48
+
49
+ it 'should squish otu abundance matrix by same name' do
50
+ `./bin/lederhosen squish --csv-file=#{test_dir}/named_otus.csv`
51
+ $?.success?.should be_true
52
+ end
53
+ end
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: lederhosen
3
3
  version: !ruby/object:Gem::Version
4
- hash: 29
4
+ hash: 19
5
5
  prerelease:
6
6
  segments:
7
7
  - 0
8
8
  - 1
9
- - 3
10
- version: 0.1.3
9
+ - 4
10
+ version: 0.1.4
11
11
  platform: ruby
12
12
  authors:
13
13
  - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
15
15
  bindir: bin
16
16
  cert_chain: []
17
17
 
18
- date: 2012-07-13 00:00:00 Z
18
+ date: 2012-07-14 00:00:00 Z
19
19
  dependencies:
20
20
  - !ruby/object:Gem::Dependency
21
21
  name: dna
@@ -137,7 +137,6 @@ files:
137
137
  - lib/lederhosen/helpers.rb
138
138
  - lib/lederhosen/tasks/add_names.rb
139
139
  - lib/lederhosen/tasks/cluster.rb
140
- - lib/lederhosen/tasks/hierarchical.rb
141
140
  - lib/lederhosen/tasks/join.rb
142
141
  - lib/lederhosen/tasks/k_filter.rb
143
142
  - lib/lederhosen/tasks/name.rb
@@ -154,6 +153,9 @@ files:
154
153
  - spec/data/ILT_L_9_B_001_3.txt
155
154
  - spec/data/ILT_L_9_B_002_1.txt
156
155
  - spec/data/ILT_L_9_B_002_3.txt
156
+ - spec/data/blast_out.txt
157
+ - spec/data/blat.txt
158
+ - spec/data/otus.csv
157
159
  - spec/helpers_spec.rb
158
160
  - spec/misc_spec.rb
159
161
  - spec/pipeline_spec.rb
@@ -196,6 +198,9 @@ test_files:
196
198
  - spec/data/ILT_L_9_B_001_3.txt
197
199
  - spec/data/ILT_L_9_B_002_1.txt
198
200
  - spec/data/ILT_L_9_B_002_3.txt
201
+ - spec/data/blast_out.txt
202
+ - spec/data/blat.txt
203
+ - spec/data/otus.csv
199
204
  - spec/helpers_spec.rb
200
205
  - spec/misc_spec.rb
201
206
  - spec/pipeline_spec.rb
data/lib/lederhosen/tasks/hierarchical.rb DELETED
@@ -1,40 +0,0 @@
1
- ##
2
- # HIERARCHICAL CLUSTERING FTW
3
- #
4
-
5
- module Lederhosen
6
- class CLI
7
-
8
- desc "h_cluster",
9
- "--input=sorted.fasta --identity=0.80 --output=clusters.uc --identities=0.80 0.90 0.95"
10
-
11
- method_option :input, :type => :string, :required => true
12
- method_option :out_dir, :type => :string, :required => true
13
- method_option :identities, :type => :array, :required => true
14
-
15
- def h_cluster
16
- out_dir = options[:out_dir]
17
- input = options[:input]
18
- identities = options[:identities].map(&:to_f).sort
19
-
20
- `mkdir -p #{out_dir}`
21
-
22
- # initial clustering
23
- i = identities.shift
24
- clusters = File.join(out_dir, "clusters_#{i}.uc")
25
- clusters_filtered = File.join(out_dir, "clusters_#{i}.uc.filtered")
26
-
27
- # cluster
28
- invoke :cluster, [], { :input => input, :output => clusters, :identity => i }
29
-
30
- # filter
31
- invoke :uc_filter, [], { :input => clusters, :output => clusters_filtered }
32
-
33
- # get reads for each cluster
34
- invoke :split, [], { :clusters => clusters_filtered, :reads => input }
35
-
36
- [t1, t2, t3].map(&:call)
37
- end
38
-
39
- end
40
- end