parse_fasta 1.6.2 → 1.7.0
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- checksums.yaml +13 -5
- data/.yardopts +1 -0
- data/README.md +9 -1
- data/lib/parse_fasta/fasta_file.rb +17 -0
- data/lib/parse_fasta/fastq_file.rb +24 -5
- data/lib/parse_fasta/seq_file.rb +24 -3
- data/lib/parse_fasta/version.rb +1 -1
- data/parse_fasta.gemspec +1 -0
- data/spec/lib/fasta_file_spec.rb +16 -0
- data/spec/lib/fastq_file_spec.rb +33 -3
- data/spec/lib/seq_file_spec.rb +53 -2
- data/spec/spec_helper.rb +11 -0
- metadata +36 -21
checksums.yaml
CHANGED
@@ -1,7 +1,15 @@
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---
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-
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metadata.gz:
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-
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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4
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YjUzNjQwMGYzNDQzNWNiYzczOTFmYmE3OGY2YWI0MmJkNjhkNmE0ZA==
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5
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+
data.tar.gz: !binary |-
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+
ODFjMmIxNWE5MDc1ODE0MGUyOWRmYTg5YmFkNWJkMjE1MzUxMjg1Yg==
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SHA512:
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metadata.gz:
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-
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metadata.gz: !binary |-
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NmFmNjcwODhhM2E0NmM2NzE1OTA0NmYwOGVmZTM0NjA3Mzg4ZmUyNWUwYjNm
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+
ZTRjNmE0NWI2MTc1NWM5NTMwM2I5YjEzYzQxMjcwYTJhMjdiMmVkZmJmNWVj
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+
ZTU1ODY1OGE1ZGRiOGQ3ZGU1NTIyYWI0ZTJlN2I4YTBiMGIzOTg=
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data.tar.gz: !binary |-
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+
ZTM2YTBhNGU4N2E4ZDJkYTI1OWNiMTI5YjQ5Njc1ZTlmYTI4MzMxYWRmZDNk
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N2U0Zjk1N2M1M2YzZWMxNjk0NDZlNmIzYjFjYTAzNWQ2YjllYWQxYjk2ZDAx
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15
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+
NDRiYTc3ZjFiNzIxM2VmNjQxODlkMjgxZWQ4MTRlY2M0NjRkOWQ=
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data/.yardopts
ADDED
@@ -0,0 +1 @@
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1
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+
--markup-provider rdiscount
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data/README.md
CHANGED
@@ -27,7 +27,7 @@ lightweight than BioRuby. And more fun! ;)
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## Documentation ##
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Checkout
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-
[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.
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+
[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.7.0/frames)
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for the full api documentation.
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## Usage ##
|
@@ -60,8 +60,16 @@ What if you don't care if the input is a fastA or a fastQ? No problem!
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puts [header, seq].join "\t"
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end
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62
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63
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+
Read fasta file into a hash.
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+
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seqs = FastaFile.open(ARGV[0]).to_hash
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+
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## Versions ##
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68
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+
### 1.7 ###
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+
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Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
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+
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### 1.6 ###
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Added `SeqFile` class, which accepts either fastA or fastQ files. It
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@@ -43,6 +43,23 @@ class FastaFile < File
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super
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44
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end
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+
# Returns the records in the fasta file as a hash map with the
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# headers as keys and the Sequences as values.
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+
#
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# @example Read a fastA into a hash table.
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# seqs = FastaFile.open('reads.fa').to_hash
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+
#
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# @return [Hash] A hash with headers as keys, sequences as the
|
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+
# values (Sequence objects)
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+
def to_hash
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hash = {}
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self.each_record do |head, seq|
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hash[head] = seq
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end
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hash
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end
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+
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# Analagous to IO#each_line, #each_record is used to go through a
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# fasta file record by record. It will accept gzipped files as well.
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#
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@@ -22,6 +22,25 @@ require 'zlib'
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# format files. Gzipped files are no problem.
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class FastqFile < File
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# Returns the records in the fastq file as a hash map with the
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# headers as keys pointing to a hash map like so
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# { "seq1" => { head: "seq1", seq: "ACTG", desc: "", qual: "II3*"} }
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+
#
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# @example Read a fastQ into a hash table.
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# seqs = FastqFile.open('reads.fq.gz').to_hash
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+
#
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+
# @return [Hash] A hash with headers as keys, and a hash map as the
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+
# value with keys :head, :seq, :desc, :qual, for header, sequence,
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+
# description, and quality.
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+
def to_hash
|
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+
hash = {}
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+
self.each_record do |head, seq, desc, qual|
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+
hash[head] = { head: head, seq: seq, desc: desc, qual: qual }
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+
end
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hash
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+
end
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+
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# Analagous to IO#each_line, #each_record is used to go through a
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# fastq file record by record. It will accept gzipped files as well.
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#
|
@@ -33,7 +52,7 @@ class FastqFile < File
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# FastqFile.open('reads.fq.gz').each_record do |head, seq, desc, qual|
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# # do some fun stuff here!
|
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# end
|
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-
#
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+
#
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# @yield The header, sequence, description and quality string for
|
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# each record in the fastq file to the block
|
39
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# @yieldparam header [String] The header of the fastq record without
|
@@ -54,8 +73,8 @@ class FastqFile < File
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73
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f = Zlib::GzipReader.open(self)
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rescue Zlib::GzipFile::Error => e
|
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f = self
|
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-
end
|
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-
|
76
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+
end
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+
|
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|
f.each_line do |line|
|
60
79
|
line.chomp!
|
61
80
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|
@@ -70,10 +89,10 @@ class FastqFile < File
|
|
70
89
|
quality = Quality.new(line)
|
71
90
|
yield(header, sequence, description, quality)
|
72
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end
|
73
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-
|
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+
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count += 1
|
75
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end
|
76
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-
|
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+
|
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96
|
f.close if f.instance_of?(Zlib::GzipReader)
|
78
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return f
|
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end
|
data/lib/parse_fasta/seq_file.rb
CHANGED
@@ -20,6 +20,27 @@
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20
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# depending on what the user provides. Handles, gzipped files.
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21
21
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class SeqFile < File
|
22
22
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|
23
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+
# Returns the records in the sequence file as a hash map with the
|
24
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+
# headers as keys and the Sequences as values. For a fastq file,
|
25
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+
# acts the same as `FastaFile#to_hash`
|
26
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+
#
|
27
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+
# @example Read a fastA into a hash table.
|
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+
# seqs = SeqFile.open('reads.fa').to_hash
|
29
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+
#
|
30
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+
# @return [Hash] A hash with headers as keys, sequences as the
|
31
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+
# values (Sequence objects)
|
32
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+
def to_hash
|
33
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+
first_char = get_first_char(self)
|
34
|
+
|
35
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+
if first_char == '>'
|
36
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+
FastaFile.open(self).to_hash
|
37
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+
elsif first_char == '@'
|
38
|
+
FastqFile.open(self).to_hash
|
39
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+
else
|
40
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+
raise ArgumentError, "Input does not look like FASTA or FASTQ"
|
41
|
+
end
|
42
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+
end
|
43
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+
|
23
44
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# Analagous to IO#each_line, #each_record will go through a fastA or
|
24
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|
# fastQ file record by record.
|
25
46
|
#
|
@@ -54,7 +75,7 @@ class SeqFile < File
|
|
54
75
|
# @yieldparam sequence [Sequence] The sequence of the record.
|
55
76
|
def each_record
|
56
77
|
first_char = get_first_char(self)
|
57
|
-
|
78
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+
|
58
79
|
if first_char == '>'
|
59
80
|
FastaFile.open(self).each_record do |header, sequence|
|
60
81
|
yield(header, sequence)
|
@@ -65,7 +86,7 @@ class SeqFile < File
|
|
65
86
|
end
|
66
87
|
else
|
67
88
|
raise ArgumentError, "Input does not look like FASTA or FASTQ"
|
68
|
-
end
|
89
|
+
end
|
69
90
|
end
|
70
91
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|
71
92
|
private
|
@@ -75,7 +96,7 @@ class SeqFile < File
|
|
75
96
|
handle = Zlib::GzipReader.open(f)
|
76
97
|
rescue Zlib::GzipFile::Error => e
|
77
98
|
handle = f
|
78
|
-
end
|
99
|
+
end
|
79
100
|
|
80
101
|
handle.each_line.peek[0]
|
81
102
|
end
|
data/lib/parse_fasta/version.rb
CHANGED
data/parse_fasta.gemspec
CHANGED
@@ -28,5 +28,6 @@ Gem::Specification.new do |spec|
|
|
28
28
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spec.add_development_dependency "rspec", "~> 2.14"
|
29
29
|
spec.add_development_dependency "bio", "~> 1.4"
|
30
30
|
spec.add_development_dependency "yard", "~> 0.8"
|
31
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+
spec.add_development_dependency "rdiscount"
|
31
32
|
spec.add_development_dependency "coveralls", "~> 0.7"
|
32
33
|
end
|
data/spec/lib/fasta_file_spec.rb
CHANGED
@@ -44,6 +44,22 @@ describe FastaFile do
|
|
44
44
|
end
|
45
45
|
end
|
46
46
|
|
47
|
+
describe "#to_hash" do
|
48
|
+
let(:records) { Helpers::RECORDS_MAP }
|
49
|
+
let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz" }
|
50
|
+
let(:fasta) { FastaFile.open(fname) }
|
51
|
+
|
52
|
+
it "reads the records into a hash: header as key and seq as val" do
|
53
|
+
expect(fasta.to_hash).to eq records
|
54
|
+
end
|
55
|
+
|
56
|
+
it "passes the values as Sequence objects" do
|
57
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+
expect(
|
58
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+
fasta.to_hash.values.all? { |val| val.instance_of? Sequence }
|
59
|
+
).to eq true
|
60
|
+
end
|
61
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+
end
|
62
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+
|
47
63
|
describe "#each_record" do
|
48
64
|
let(:records) { Helpers::RECORDS }
|
49
65
|
|
data/spec/lib/fastq_file_spec.rb
CHANGED
@@ -43,9 +43,40 @@ describe FastqFile do
|
|
43
43
|
expect(qual).to be_an_instance_of Quality
|
44
44
|
end
|
45
45
|
end
|
46
|
+
end
|
47
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+
|
48
|
+
describe "#to_hash" do
|
49
|
+
let(:records) {
|
50
|
+
{ "seq1" => { head: "seq1",
|
51
|
+
seq: "AACCTTGG",
|
52
|
+
desc: "",
|
53
|
+
qual: ")#3gTqN8" },
|
54
|
+
"seq2 apples" => { head: "seq2 apples",
|
55
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+
seq: "ACTG",
|
56
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+
desc: "seq2 apples",
|
57
|
+
qual: "*ujM" }
|
58
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+
}
|
59
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+
}
|
60
|
+
let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz" }
|
61
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+
let(:fastq) { FastqFile.open(fname) }
|
62
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+
|
63
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+
it "reads the records into a hash: header as key and seq as val" do
|
64
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+
expect(fastq.to_hash).to eq records
|
65
|
+
end
|
66
|
+
|
67
|
+
it "passes the seqs as Sequence objects" do
|
68
|
+
expect(
|
69
|
+
fastq.to_hash.values.all? { |val| val[:seq].instance_of? Sequence }
|
70
|
+
).to eq true
|
71
|
+
end
|
46
72
|
|
73
|
+
it "passes the quals as Quality objects" do
|
74
|
+
expect(
|
75
|
+
fastq.to_hash.values.all? { |val| val[:qual].instance_of? Quality }
|
76
|
+
).to eq true
|
77
|
+
end
|
47
78
|
end
|
48
|
-
|
79
|
+
|
49
80
|
context "with a 4 line per record fastq file" do
|
50
81
|
describe "#each_record" do
|
51
82
|
context "with a gzipped file" do
|
@@ -80,6 +111,5 @@ describe FastqFile do
|
|
80
111
|
end
|
81
112
|
end
|
82
113
|
end
|
83
|
-
end
|
114
|
+
end
|
84
115
|
end
|
85
|
-
|
data/spec/lib/seq_file_spec.rb
CHANGED
@@ -19,6 +19,57 @@
|
|
19
19
|
require 'spec_helper'
|
20
20
|
|
21
21
|
describe SeqFile do
|
22
|
+
|
23
|
+
describe "#to_hash" do
|
24
|
+
context "when input is a fasta file" do
|
25
|
+
let(:records) { Helpers::RECORDS_MAP }
|
26
|
+
let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz" }
|
27
|
+
let(:fasta) { SeqFile.open(fname) }
|
28
|
+
|
29
|
+
it "reads the records into a hash: header as key and seq as val" do
|
30
|
+
expect(fasta.to_hash).to eq records
|
31
|
+
end
|
32
|
+
|
33
|
+
it "passes the values as Sequence objects" do
|
34
|
+
expect(
|
35
|
+
fasta.to_hash.values.all? { |val| val.instance_of? Sequence }
|
36
|
+
).to eq true
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
context "when input is a fastq file" do
|
41
|
+
let(:records) {
|
42
|
+
{ "seq1" => { head: "seq1",
|
43
|
+
seq: "AACCTTGG",
|
44
|
+
desc: "",
|
45
|
+
qual: ")#3gTqN8" },
|
46
|
+
"seq2 apples" => { head: "seq2 apples",
|
47
|
+
seq: "ACTG",
|
48
|
+
desc: "seq2 apples",
|
49
|
+
qual: "*ujM" }
|
50
|
+
}
|
51
|
+
}
|
52
|
+
let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz" }
|
53
|
+
let(:fastq) { SeqFile.open(fname) }
|
54
|
+
|
55
|
+
it "reads the records into a hash: header as key and seq as val" do
|
56
|
+
expect(fastq.to_hash).to eq records
|
57
|
+
end
|
58
|
+
|
59
|
+
it "passes the seqs as Sequence objects" do
|
60
|
+
expect(
|
61
|
+
fastq.to_hash.values.all? { |val| val[:seq].instance_of? Sequence }
|
62
|
+
).to eq true
|
63
|
+
end
|
64
|
+
|
65
|
+
it "passes the quals as Quality objects" do
|
66
|
+
expect(
|
67
|
+
fastq.to_hash.values.all? { |val| val[:qual].instance_of? Quality }
|
68
|
+
).to eq true
|
69
|
+
end
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
22
73
|
describe "#each_record" do
|
23
74
|
|
24
75
|
context "when input is a fasta file" do
|
@@ -138,8 +189,8 @@ describe SeqFile do
|
|
138
189
|
err_msg = "Input does not look like FASTA or FASTQ"
|
139
190
|
|
140
191
|
expect { SeqFile.open(fname).each_record do |h, s|
|
141
|
-
|
142
|
-
|
192
|
+
puts [h, s].join ' '
|
193
|
+
end
|
143
194
|
}.to raise_error(ArgumentError, err_msg)
|
144
195
|
end
|
145
196
|
end
|
data/spec/spec_helper.rb
CHANGED
@@ -31,6 +31,17 @@ module Helpers
|
|
31
31
|
["seq3", "yyyyyyyyyyyyyyyNNN"],
|
32
32
|
["empty seq at end", ""]]
|
33
33
|
|
34
|
+
RECORDS_MAP = {
|
35
|
+
"empty seq at beginning" => "",
|
36
|
+
"seq1 is fun" => "AACTGGNNN",
|
37
|
+
"seq2" => "AATCCTGNNN",
|
38
|
+
"empty seq 1" => "",
|
39
|
+
"empty seq 2" => "",
|
40
|
+
"seq3" => "yyyyyyyyyyyyyyyNNN",
|
41
|
+
"empty seq at end" => ""
|
42
|
+
}
|
43
|
+
|
44
|
+
|
34
45
|
TRUTHY_RECORDS = [["empty seq at beginning", []],
|
35
46
|
["seq1 is fun", ["AACTGGNNN"]],
|
36
47
|
["seq2", ["AAT", "CCTGNNN"]],
|
metadata
CHANGED
@@ -1,97 +1,111 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: parse_fasta
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.
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4
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+
version: 1.7.0
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Ryan Moore
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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11
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-
date: 2015-
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11
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+
date: 2015-07-11 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
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name: bundler
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15
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requirement: !ruby/object:Gem::Requirement
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requirements:
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17
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-
- -
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17
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+
- - ~>
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18
18
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- !ruby/object:Gem::Version
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version: '1.6'
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20
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type: :development
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21
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prerelease: false
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22
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version_requirements: !ruby/object:Gem::Requirement
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23
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requirements:
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24
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-
- -
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24
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+
- - ~>
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25
25
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- !ruby/object:Gem::Version
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26
26
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version: '1.6'
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27
27
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- !ruby/object:Gem::Dependency
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28
28
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name: rake
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29
29
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requirement: !ruby/object:Gem::Requirement
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30
30
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requirements:
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31
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-
- -
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31
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+
- - ~>
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32
32
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- !ruby/object:Gem::Version
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33
33
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version: '10.3'
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34
34
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type: :development
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35
35
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prerelease: false
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36
36
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version_requirements: !ruby/object:Gem::Requirement
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37
37
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requirements:
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38
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-
- -
|
38
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+
- - ~>
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39
39
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- !ruby/object:Gem::Version
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40
40
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version: '10.3'
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41
41
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- !ruby/object:Gem::Dependency
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42
42
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name: rspec
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43
43
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requirement: !ruby/object:Gem::Requirement
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44
44
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requirements:
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45
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-
- -
|
45
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+
- - ~>
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46
46
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- !ruby/object:Gem::Version
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47
47
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version: '2.14'
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48
48
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type: :development
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49
49
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prerelease: false
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50
50
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version_requirements: !ruby/object:Gem::Requirement
|
51
51
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requirements:
|
52
|
-
- -
|
52
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+
- - ~>
|
53
53
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- !ruby/object:Gem::Version
|
54
54
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version: '2.14'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
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name: bio
|
57
57
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requirement: !ruby/object:Gem::Requirement
|
58
58
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requirements:
|
59
|
-
- -
|
59
|
+
- - ~>
|
60
60
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- !ruby/object:Gem::Version
|
61
61
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version: '1.4'
|
62
62
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type: :development
|
63
63
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prerelease: false
|
64
64
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version_requirements: !ruby/object:Gem::Requirement
|
65
65
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requirements:
|
66
|
-
- -
|
66
|
+
- - ~>
|
67
67
|
- !ruby/object:Gem::Version
|
68
68
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version: '1.4'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
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name: yard
|
71
71
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requirement: !ruby/object:Gem::Requirement
|
72
72
|
requirements:
|
73
|
-
- -
|
73
|
+
- - ~>
|
74
74
|
- !ruby/object:Gem::Version
|
75
75
|
version: '0.8'
|
76
76
|
type: :development
|
77
77
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prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
|
-
- -
|
80
|
+
- - ~>
|
81
81
|
- !ruby/object:Gem::Version
|
82
82
|
version: '0.8'
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: rdiscount
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - ! '>='
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: '0'
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - ! '>='
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: '0'
|
83
97
|
- !ruby/object:Gem::Dependency
|
84
98
|
name: coveralls
|
85
99
|
requirement: !ruby/object:Gem::Requirement
|
86
100
|
requirements:
|
87
|
-
- -
|
101
|
+
- - ~>
|
88
102
|
- !ruby/object:Gem::Version
|
89
103
|
version: '0.7'
|
90
104
|
type: :development
|
91
105
|
prerelease: false
|
92
106
|
version_requirements: !ruby/object:Gem::Requirement
|
93
107
|
requirements:
|
94
|
-
- -
|
108
|
+
- - ~>
|
95
109
|
- !ruby/object:Gem::Version
|
96
110
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version: '0.7'
|
97
111
|
description: Provides nice, programmatic access to fasta and fastq files, as well
|
@@ -102,9 +116,10 @@ executables: []
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|
102
116
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extensions: []
|
103
117
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extra_rdoc_files: []
|
104
118
|
files:
|
105
|
-
-
|
106
|
-
-
|
107
|
-
-
|
119
|
+
- .coveralls.yml
|
120
|
+
- .gitignore
|
121
|
+
- .travis.yml
|
122
|
+
- .yardopts
|
108
123
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- COPYING
|
109
124
|
- Gemfile
|
110
125
|
- README.md
|
@@ -131,7 +146,7 @@ files:
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|
131
146
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- test_files/test.fq.gz
|
132
147
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homepage: https://github.com/mooreryan/parse_fasta
|
133
148
|
licenses:
|
134
|
-
- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
149
|
+
- ! 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
135
150
|
metadata: {}
|
136
151
|
post_install_message:
|
137
152
|
rdoc_options: []
|
@@ -139,17 +154,17 @@ require_paths:
|
|
139
154
|
- lib
|
140
155
|
required_ruby_version: !ruby/object:Gem::Requirement
|
141
156
|
requirements:
|
142
|
-
- -
|
157
|
+
- - ! '>='
|
143
158
|
- !ruby/object:Gem::Version
|
144
159
|
version: 1.9.3
|
145
160
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
146
161
|
requirements:
|
147
|
-
- -
|
162
|
+
- - ! '>='
|
148
163
|
- !ruby/object:Gem::Version
|
149
164
|
version: '0'
|
150
165
|
requirements: []
|
151
166
|
rubyforge_project:
|
152
|
-
rubygems_version: 2.4.
|
167
|
+
rubygems_version: 2.4.8
|
153
168
|
signing_key:
|
154
169
|
specification_version: 4
|
155
170
|
summary: Easy-peasy parsing of fasta & fastq files!
|