dna 0.2.0 → 0.2.1
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- data/dna.gemspec +2 -2
- data/lib/dna/dna.rb +2 -2
- data/lib/dna/phred.rb +1 -1
- data/lib/dna/version.rb +1 -1
- data/readme.md +28 -2
- data/spec/phred_spec.rb +4 -3
- metadata +3 -3
data/dna.gemspec
CHANGED
@@ -5,11 +5,11 @@
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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 = "dna"
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8
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-
s.version = "0.2.
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8
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+
s.version = "0.2.1"
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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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12
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-
s.date = "2012-12-
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12
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+
s.date = "2012-12-19"
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13
13
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s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
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14
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s.email = "harekrishna@gmail.com"
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15
15
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s.executables = ["dna"]
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data/lib/dna/dna.rb
CHANGED
data/lib/dna/phred.rb
CHANGED
data/lib/dna/version.rb
CHANGED
data/readme.md
CHANGED
@@ -53,9 +53,10 @@ File.open('sequences.qseq') do |handle|
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53
53
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puts records.first.inspect
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54
54
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end
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55
55
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56
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-
# Even supports Gzip
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56
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+
# Even supports Gzip but you must specify the format
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57
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+
# (can't rewind in Gzip)
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57
58
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File.open('sequences.fasta.gz') do |handle|
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58
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-
records = Dna.new handle
|
59
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+
records = Dna.new handle, :format => :fasta
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59
60
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60
61
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records.each do |record|
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61
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puts record.length
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@@ -63,6 +64,31 @@ File.open('sequences.fasta.gz') do |handle|
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63
64
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end
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64
65
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```
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65
66
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67
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+
## Support for PHRED score parsing
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68
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+
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69
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+
```ruby
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70
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+
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71
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+
# Illumina > 1.3)
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72
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+
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73
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+
record.illumina_qualities # => [31, ..., 37]
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74
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+
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75
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+
# Error probabilities
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76
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+
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77
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+
record.illumina_probabilities
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78
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+
# => [1.0, 0.7943282347242815, ..., 0.3981071705534972]
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79
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+
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80
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+
# Solexa + Illumina =< 1.3
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81
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+
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82
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+
record.solexa_qualities
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83
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+
record.solexa_probabilities
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84
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+
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85
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+
# Sanger
|
86
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+
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87
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+
record.sanger_qualities
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88
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+
record.sanger_probabilities
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89
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+
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90
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+
```
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91
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+
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66
92
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## Bonus Feature
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67
93
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68
94
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The DNA gem is also a command-line tool with grep-like capabilities. Print records with (Ruby) regexp match in header.
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data/spec/phred_spec.rb
CHANGED
@@ -1,6 +1,7 @@
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1
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+
# XXX should probably use the actual record objects
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1
2
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class TestRecord
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2
3
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include Phred
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3
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-
attr_accessor :
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4
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+
attr_accessor :quality
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4
5
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end
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5
6
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6
7
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##
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@@ -62,12 +63,12 @@ describe Phred do
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62
63
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format_definitions.each_pair do |type, properties|
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63
64
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|
64
65
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it "should properly convert #{type} raw ascii PHRED scores to integers" do
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65
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-
test_record.
|
66
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+
test_record.quality = properties[:string]
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66
67
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test_record.send(:"#{type}_scores").should == properties[:scores]
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67
68
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end
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68
69
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|
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70
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it "should properly convert #{type.to_s} raw ascii PHRED scores to probabilities" do
|
70
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-
test_record.
|
71
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+
test_record.quality = properties[:string]
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71
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test_record.send(:"#{type}_probabilities").should == properties[:probabilities]
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72
73
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end
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73
74
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: dna
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.2.
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4
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+
version: 0.2.1
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -9,7 +9,7 @@ authors:
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9
9
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autorequire:
|
10
10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date: 2012-12-
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12
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+
date: 2012-12-19 00:00:00.000000000 Z
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13
13
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dependencies:
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14
14
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- !ruby/object:Gem::Dependency
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15
15
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name: jeweler
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@@ -74,7 +74,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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|
74
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version: '0'
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75
75
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segments:
|
76
76
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- 0
|
77
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-
hash:
|
77
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+
hash: 1149140625798689145
|
78
78
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required_rubygems_version: !ruby/object:Gem::Requirement
|
79
79
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none: false
|
80
80
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requirements:
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