lederhosen 1.8.1 → 1.8.2
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- data/lederhosen.gemspec +3 -9
- data/lib/lederhosen/tasks/otu_table.rb +3 -0
- data/lib/lederhosen/version.rb +1 -1
- data/spec/cli_spec.rb +5 -15
- data/spec/data/trimmed/ILT_L_9_B_001.fasta +1596 -0
- data/spec/no_tasks_spec.rb +19 -24
- metadata +3 -9
- data/spec/data/ILT_L_9_B_001_1.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_001_3.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_002_1.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_002_3.txt.gz +0 -0
- data/spec/data/example.fastq +0 -400
- data/spec/data/trimmed_sizes.txt +0 -100
- data/spec/trimmer_spec.rb +0 -85
data/lederhosen.gemspec
CHANGED
@@ -5,7 +5,7 @@
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5
5
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6
6
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Gem::Specification.new do |s|
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7
7
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s.name = "lederhosen"
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8
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-
s.version = "1.8.
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8
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+
s.version = "1.8.2"
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9
9
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10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Austin G. Davis-Richardson"]
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@@ -43,16 +43,10 @@ Gem::Specification.new do |s|
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43
43
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"scripts/otu_ref_picking/readme.md",
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"scripts/readme.md",
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45
45
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"spec/cli_spec.rb",
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46
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-
"spec/data/ILT_L_9_B_001_1.txt.gz",
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47
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-
"spec/data/ILT_L_9_B_001_3.txt.gz",
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48
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-
"spec/data/ILT_L_9_B_002_1.txt.gz",
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49
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-
"spec/data/ILT_L_9_B_002_3.txt.gz",
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50
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-
"spec/data/example.fastq",
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51
46
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"spec/data/test.uc",
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52
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-
"spec/data/
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47
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+
"spec/data/trimmed/ILT_L_9_B_001.fasta",
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53
48
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"spec/no_tasks_spec.rb",
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54
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-
"spec/spec_helper.rb"
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55
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-
"spec/trimmer_spec.rb"
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49
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+
"spec/spec_helper.rb"
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56
50
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]
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57
51
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s.homepage = "http://audy.github.com/lederhosen"
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58
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s.licenses = ["MIT"]
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data/lib/lederhosen/version.rb
CHANGED
data/spec/cli_spec.rb
CHANGED
@@ -12,30 +12,20 @@ describe Lederhosen::CLI do
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12
12
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$?.success?.should be_true
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13
13
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end
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14
14
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15
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-
it 'should trim paired QSEQ reads' do
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16
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-
`./bin/lederhosen trim --reads-dir=spec/data/IL*.txt.gz --out-dir=#{$test_dir}/trimmed`
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17
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-
$?.success?.should be_true
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18
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-
end
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19
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-
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20
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-
it 'should trim paired, interleaved FASTQ reads' do
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21
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-
`./bin/lederhosen trim --reads-dir=spec/data/example.fastq --out-dir=#{$test_dir}/trimmed --read-type fastq`
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22
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-
$?.success?.should be_true
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23
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-
end
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24
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-
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25
15
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it 'can create a usearch udb using usearch' do
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26
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-
`./bin/lederhosen make_udb --input
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16
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+
`./bin/lederhosen make_udb --input spec/data/trimmed/ILT_L_9_B_001.fasta --output #{$test_dir}/test_db.udb`
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27
17
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$?.success?.should be_true
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28
18
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end
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29
19
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30
20
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it 'can (dry run) cluster reads using usearch and output usearch cmd to stdout' do
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31
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-
stdout = `./bin/lederhosen cluster --dry-run --input
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21
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+
stdout = `./bin/lederhosen cluster --dry-run --input spec/data/trimmed/ILT_L_9_B_001.fasta --database #{$test_dir}/test_db.udb --identity 0.95 --output #{$test_dir}/clusters.uc`
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32
22
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stdout.should match /^usearch/
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33
23
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$?.success?.should be_true
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34
24
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File.exists?(File.join($test_dir, 'clusters.uc')).should be_false
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35
25
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end
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36
26
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37
27
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it 'can cluster reads using usearch' do
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38
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-
`./bin/lederhosen cluster --input
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28
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+
`./bin/lederhosen cluster --input spec/data/trimmed/ILT_L_9_B_001.fasta --database #{$test_dir}/test_db.udb --identity 0.95 --output #{$test_dir}/clusters.uc`
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39
29
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$?.success?.should be_true
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40
30
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File.exists?(File.join($test_dir, 'clusters.uc')).should be_true
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41
31
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end
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@@ -57,12 +47,12 @@ describe Lederhosen::CLI do
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57
47
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end
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58
48
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59
49
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it 'should split a fasta file into smaller fasta files (optionally gzipped)' do
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60
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-
`./bin/lederhosen split_fasta --input
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50
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+
`./bin/lederhosen split_fasta --input=spec/data/trimmed/ILT_L_9_B_001.fasta --out-dir=#{$test_dir}/split/ --gzip true -n 100`
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61
51
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$?.success?.should be_true
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62
52
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end
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63
53
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64
54
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it 'should print representative sequences from uc files' do
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65
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-
`./bin/lederhosen get_reps --input=#{$test_dir}/clusters.uc --database
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55
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+
`./bin/lederhosen get_reps --input=#{$test_dir}/clusters.uc --database=spec/data/trimmed/ILT_L_9_B_001.fasta --output=#{$test_dir}/representatives.fasta`
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66
56
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end
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67
57
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68
58
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it 'should create a fasta file containing representative reads for each cluster'
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