dna 0.0.3 → 0.0.4
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- data/lib/dna.rb +2 -2
- data/spec/dna_spec.rb +9 -6
- metadata +1 -1
data/lib/dna.rb
CHANGED
@@ -57,7 +57,7 @@ class Dna # iterator
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57
57
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n = c.next
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58
58
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case n
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59
59
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when 0
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60
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-
params[:name] = line.strip
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60
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+
params[:name] = line.strip[1..-1]
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61
61
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when 1
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62
62
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params[:sequence] = line.strip
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63
63
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when 2
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@@ -143,7 +143,7 @@ class QSEQ < Record
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143
143
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def initialize(args={})
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144
144
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# These are the properties defined by the qseq spec
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145
145
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# they must be in the same order that they appear in the tab-separated qseq file
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146
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-
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146
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+
@properties = :machine, :run, :lane, :tile, :x, :y, :index, :read_no, :sequence, :quality, :filtered
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147
147
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@machine = args[:machine]
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148
148
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@run = args[:run]
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149
149
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@lane = args[:lane]
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data/spec/dna_spec.rb
CHANGED
@@ -7,16 +7,18 @@ describe Dna do
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7
7
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let (:fastq) { Dna.new @fastq_file, format: 'fastq' }
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8
8
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let (:qseq) { Dna.new @qseq_file, format: 'qseq' }
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9
9
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10
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-
it 'can parse a crappily formatted fasta file' do
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11
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-
fasta.to_a
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10
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+
it 'can properly parse a crappily formatted fasta file' do
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11
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+
records = fasta.to_a
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12
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+
records[1].name.should == '2'
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12
13
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end
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13
14
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14
15
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it 'generates fasta objects from a fasta file' do
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15
16
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fasta.first.class.should == Fasta
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16
17
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end
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17
18
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18
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-
it 'can parse fastq format' do
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19
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-
fastq.to_a
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19
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+
it 'can properly parse fastq format' do
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20
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+
records = fastq.to_a
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21
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+
records[1].name.should == '2'
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20
22
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end
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21
23
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22
24
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it 'generates fastq objects from a fasta file' do
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@@ -27,8 +29,9 @@ describe Dna do
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27
29
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fastq.first.sequence.should_not be_nil
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28
30
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end
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29
31
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|
30
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-
it 'can parse qseq' do
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31
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-
qseq.to_a
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32
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+
it 'can properly parse qseq format' do
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33
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+
records = qseq.to_a
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34
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+
records[1].sequence.should == 'GTGTGCCAGCAGCCGCGGTAATACAGAGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCCGCTAAGCCGAACGTGAAATCCC'
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32
35
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end
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33
36
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34
37
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it 'generates qseq objects from a qseq file' do
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