parse_fasta 1.4.0 → 1.5.0
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- checksums.yaml +13 -5
- data/README.md +5 -1
- data/lib/parse_fasta/fasta_file.rb +27 -14
- data/lib/parse_fasta/fastq_file.rb +21 -6
- data/lib/parse_fasta/quality.rb +1 -1
- data/lib/parse_fasta/sequence.rb +1 -1
- data/lib/parse_fasta/version.rb +2 -2
- data/lib/parse_fasta.rb +1 -1
- data/parse_fasta.gemspec +5 -2
- data/spec/lib/fasta_file_spec.rb +67 -26
- data/spec/lib/fastq_file_spec.rb +57 -22
- data/spec/lib/quality_spec.rb +1 -1
- data/spec/lib/sequence_spec.rb +1 -1
- data/spec/spec_helper.rb +1 -1
- data/test_files/benchmark.rb +1 -1
- data/test_files/test.fa.gz +0 -0
- data/test_files/test.fq.gz +0 -0
- metadata +21 -18
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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+
YTBkNDczMWQyMjI5YzNkMmEwY2M1MWY3ODRlMzI3ZjE2MThhM2FkMw==
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data.tar.gz: !binary |-
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+
YzNlOGU2Y2FiMDlhMjMxMDkxNTE2Y2NjMzdlOWE2MmUzOWRlMzdiMw==
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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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NGE2NGMyOThlODMzODk0M2ZjMTI2YjI3ZWY4MWVmMTgwODQzNjdhNmI1MjM2
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+
NGNkNmFmODEzMTgxMTA1ZWIyN2NlZTBmZjg4NDgzZjEyMjE4ZGY1MDM0ZjBj
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+
OGE3NTFiNzE2YjEyNDJlN2VmYjdlYWY1YmUwZTI4OGE3MmE5N2I=
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data.tar.gz: !binary |-
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ZjYwMzM2OWQ2MjA2MjE1ZTg4YWUyODdkZWMyODY4NjVhNjk1NDEwNGIwZmMz
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YTJlM2U5YjFkMWI2MTNiZjEzMGY1MWIyZjQ2ZDZhOWFhZDBkMTk5NzhkMzg3
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+
OTlhZDYyN2QxMThhNmU0ZDRiY2U4ODllMmVkNzZlY2YzNjJlMDc=
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data/README.md
CHANGED
@@ -29,7 +29,7 @@ and over.
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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/1.5.0/frames)
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to see the full documentation.
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## Usage ##
|
@@ -58,6 +58,10 @@ Now we can parse fastq files as well!
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## Versions ##
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### 1.5.0 ###
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+
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Now accepts gzipped files. Huzzah!
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### 1.4.0 ###
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Added methods:
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@@ -1,4 +1,4 @@
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-
# Copyright 2014 Ryan Moore
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# Copyright 2014, 2015 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
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@@ -16,23 +16,26 @@
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# You should have received a copy of the GNU General Public License
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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-
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+
require 'zlib'
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# Provides simple interface for parsing fasta format files. Gzipped
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# files are no problem.
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class FastaFile < File
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-
# Analagous to
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-
# fasta file record by record.
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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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# @param separate_lines [Object] If truthy, separate lines of record
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-
# into an array, but if falsy, yield a Sequence
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-
# sequence instead.
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# into an array of Sequences, but if falsy, yield a Sequence
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# object for the sequence instead.
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#
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-
# @example Parsing a fasta file (default behavior)
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-
# FastaFile.open('reads.fna'
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# @example Parsing a fasta file (default behavior, gzip files are fine)
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# FastaFile.open('reads.fna.gz').each_record do |header, sequence|
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# puts [header, sequence.gc].join("\t")
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# end
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#
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# @example Parsing a fasta file (with truthy value param)
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-
# FastaFile.open('reads.fna'
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# FastaFile.open('reads.fna').each_record(1) do |header, sequence|
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# # header => 'sequence_1'
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# # sequence => ['AACTG', 'AGTCGT', ... ]
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# end
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@@ -43,22 +46,31 @@ class FastaFile < File
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# @yieldparam header [String] The header of the fasta record without
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# the leading '>'
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#
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-
# @yieldparam sequence [Sequence, Array<
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# @yieldparam sequence [Sequence, Array<Sequence>] The sequence of the
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# fasta record. If `separate_lines` is falsy (the default
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# behavior), will be Sequence, but if truthy will be
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# Array<String>.
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def each_record(separate_lines=nil)
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begin
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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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+
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if separate_lines
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-
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f.each("\n>") do |line|
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header, sequence = parse_line_separately(line)
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yield(header.strip, sequence)
|
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end
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else
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-
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+
f.each("\n>") do |line|
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header, sequence = parse_line(line)
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yield(header.strip, Sequence.new(sequence))
|
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69
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end
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end
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+
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f.close if f.instance_of?(Zlib::GzipReader)
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return f
|
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end
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|
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private
|
@@ -67,10 +79,11 @@ class FastaFile < File
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79
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end
|
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|
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def parse_line_separately(line)
|
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-
#line.chomp.split("\n", 2).map { |s| s.gsub(/>/, '') }
|
71
82
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header, sequence =
|
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line.chomp.split("\n", 2).map { |s| s.gsub(/>/, '') }
|
73
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-
sequences = sequence.split("\n")
|
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+
sequences = sequence.split("\n")
|
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.reject { |s| s.empty? }
|
86
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+
.map { |s| Sequence.new(s) }
|
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[header, sequences]
|
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end
|
@@ -1,4 +1,4 @@
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-
# Copyright 2014 Ryan Moore
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+
# Copyright 2014, 2015 Ryan Moore
|
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
|
@@ -16,15 +16,21 @@
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# You should have received a copy of the GNU General Public License
|
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
|
18
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|
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+
require 'zlib'
|
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+
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# Provides simple interface for parsing four-line-per-record fastq
|
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-
# format files.
|
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+
# format files. Gzipped files are no problem.
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class FastqFile < File
|
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|
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-
# Analagous to
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-
# fastq file record by record.
|
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+
# Analagous to IO#each_line, #each_record is used to go through a
|
26
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# fastq file record by record. It will accept gzipped files as well.
|
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#
|
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# @example Parsing a fastq file
|
27
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-
# FastqFile.open('reads.fq'
|
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+
# FastqFile.open('reads.fq').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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# @example Use the same syntax for gzipped files!
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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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#
|
@@ -43,8 +49,14 @@ class FastqFile < File
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sequence = ''
|
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description = ''
|
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quality = ''
|
52
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+
|
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begin
|
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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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-
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+
f.each_line do |line|
|
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line.chomp!
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case count % 4
|
@@ -61,5 +73,8 @@ class FastqFile < File
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count += 1
|
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end
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+
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f.close if f.instance_of?(Zlib::GzipReader)
|
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+
return f
|
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end
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end
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data/lib/parse_fasta/quality.rb
CHANGED
data/lib/parse_fasta/sequence.rb
CHANGED
data/lib/parse_fasta/version.rb
CHANGED
@@ -1,4 +1,4 @@
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1
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-
# Copyright 2014 Ryan Moore
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1
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+
# Copyright 2014, 2015 Ryan Moore
|
2
2
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# Contact: moorer@udel.edu
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3
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#
|
4
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# This file is part of parse_fasta.
|
@@ -17,5 +17,5 @@
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17
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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module ParseFasta
|
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-
VERSION = "1.
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+
VERSION = "1.5.0"
|
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21
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end
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data/lib/parse_fasta.rb
CHANGED
data/parse_fasta.gemspec
CHANGED
@@ -8,8 +8,11 @@ Gem::Specification.new do |spec|
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8
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spec.version = ParseFasta::VERSION
|
9
9
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spec.authors = ["Ryan Moore"]
|
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spec.email = ["moorer@udel.edu"]
|
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-
spec.summary = %q{Easy-peasy parsing of fasta files}
|
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-
spec.description =
|
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+
spec.summary = %q{Easy-peasy parsing of fasta & fastq files!}
|
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+
spec.description =
|
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+
"Provides nice, programmatic access to fasta " +
|
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"and fastq files, as well as providing Sequence and Quality " +
|
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"helper classes. No need for BioRuby ;)"
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spec.homepage = "https://github.com/mooreryan/parse_fasta"
|
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spec.license = "GPLv3: http://www.gnu.org/licenses/gpl.txt"
|
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data/spec/lib/fasta_file_spec.rb
CHANGED
@@ -1,4 +1,4 @@
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-
# Copyright 2014 Ryan Moore
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+
# Copyright 2014, 2015 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
|
@@ -20,41 +20,82 @@ require 'spec_helper'
|
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describe FastaFile do
|
22
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describe "#each_record" do
|
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+
let(:records) {
|
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+
[["seq1 is fun", "AACTGGNNN"],
|
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+
["seq2", "AATCCTGNNN"],
|
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["seq3", "yyyyyyyyyyyyyyyNNN"]]
|
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}
|
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|
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-
let(:
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let(:truthy_records) {
|
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[["seq1 is fun", ["AACTGGNNN"]],
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["seq2", ["AAT", "CCTGNNN"]],
|
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["seq3", ["yyyyyyyyyy", "yyyyy", "NNN"]]]
|
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}
|
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let(:f_handle) { FastaFile.open(@fname).each_record { |s| } }
|
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-
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-
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-
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-
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-
|
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+
shared_examples_for "any FastaFile" do
|
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context "with no arguments" do
|
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+
it "yields proper header and sequence for each record" do
|
39
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+
expect { |b|
|
40
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+
FastaFile.open(@fname).each_record(&b)
|
41
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+
}.to yield_successive_args(*records)
|
31
42
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end
|
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-
|
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-
expect(seqs).to eq([["seq1 is fun", "AACTGGNNN"],
|
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-
["seq2", "AATCCTGNNN"],
|
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-
["seq3", "yyyyyyyyyyyyyyyNNN"]])
|
36
43
|
|
44
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+
it "yields the sequence as a Sequence class" do
|
45
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+
FastaFile.open(@fname).each_record do |_, seq|
|
46
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+
expect(seq).to be_an_instance_of Sequence
|
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+
end
|
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+
end
|
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end
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-
|
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-
|
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-
expect
|
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-
|
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+
context "with a truthy argument" do
|
52
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+
it "yields proper header and sequence for each record" do
|
53
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+
expect { |b|
|
54
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+
FastaFile.open(@fname).each_record(1, &b)
|
55
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+
}.to yield_successive_args(*truthy_records)
|
43
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|
end
|
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-
end
|
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-
end
|
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57
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|
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-
|
48
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-
|
49
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-
|
50
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-
|
51
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-
|
58
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+
it "yields the sequence as a Sequence class" do
|
59
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+
FastaFile.open(@fname).each_record(1) do |_, seq|
|
60
|
+
all_Sequences = seq.map { |s| s.instance_of?(Sequence) }.all?
|
61
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+
expect(all_Sequences).to be true
|
62
|
+
end
|
52
63
|
end
|
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+
|
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+
end
|
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+
end
|
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+
|
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+
context "with a gzipped file" do
|
69
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+
before(:each) do
|
70
|
+
@fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz"
|
71
|
+
end
|
72
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+
|
73
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+
it_behaves_like "any FastaFile"
|
74
|
+
|
75
|
+
it "closes the GzipReader" do
|
76
|
+
expect(f_handle).to be_closed
|
77
|
+
end
|
78
|
+
|
79
|
+
it "returns GzipReader object" do
|
80
|
+
expect(f_handle).to be_an_instance_of Zlib::GzipReader
|
81
|
+
end
|
82
|
+
end
|
83
|
+
|
84
|
+
context "with a non-gzipped file" do
|
85
|
+
before(:each) do
|
86
|
+
@fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa"
|
87
|
+
end
|
88
|
+
|
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+
it_behaves_like "any FastaFile"
|
53
90
|
|
54
|
-
|
55
|
-
|
56
|
-
|
91
|
+
it "doesn't close the FastqFile (approx regular file behavior)" do
|
92
|
+
expect(f_handle).not_to be_closed
|
93
|
+
end
|
94
|
+
|
95
|
+
it "returns FastaFile object" do
|
96
|
+
expect(f_handle).to be_an_instance_of FastaFile
|
57
97
|
end
|
58
98
|
end
|
59
|
-
end
|
99
|
+
end
|
60
100
|
end
|
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+
|
data/spec/lib/fastq_file_spec.rb
CHANGED
@@ -1,4 +1,4 @@
|
|
1
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-
# Copyright 2014 Ryan Moore
|
1
|
+
# Copyright 2014, 2015 Ryan Moore
|
2
2
|
# Contact: moorer@udel.edu
|
3
3
|
#
|
4
4
|
# This file is part of parse_fasta.
|
@@ -19,32 +19,67 @@
|
|
19
19
|
require 'spec_helper'
|
20
20
|
|
21
21
|
describe FastqFile do
|
22
|
-
|
23
|
-
|
24
|
-
|
25
|
-
|
26
|
-
|
27
|
-
|
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|
-
|
29
|
-
|
30
|
-
|
22
|
+
let(:records) {
|
23
|
+
[["seq1", "AACCTTGG", "", ")#3gTqN8"],
|
24
|
+
["seq2 apples", "ACTG", "seq2 apples", "*ujM"]] }
|
25
|
+
let(:f_handle) { FastqFile.open(@fname).each_record { |s| } }
|
26
|
+
|
27
|
+
|
28
|
+
shared_examples_for "any FastqFile" do
|
29
|
+
it "yields proper header, sequence, description, and quality" do
|
30
|
+
expect { |b|
|
31
|
+
FastqFile.open(@fname).each_record(&b)
|
32
|
+
}.to yield_successive_args(records[0], records[1])
|
33
|
+
end
|
34
|
+
|
35
|
+
it "yields the sequence as a Sequence class" do
|
36
|
+
FastqFile.open(@fname).each_record do |_, seq, _, _|
|
37
|
+
expect(seq).to be_an_instance_of Sequence
|
31
38
|
end
|
39
|
+
end
|
32
40
|
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
"*ujM"]])
|
41
|
+
it "yields the quality as a Quality class" do
|
42
|
+
FastqFile.open(@fname).each_record do |_, _, _, qual|
|
43
|
+
expect(qual).to be_an_instance_of Quality
|
37
44
|
end
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
45
|
+
end
|
46
|
+
|
47
|
+
end
|
48
|
+
|
49
|
+
context "with a 4 line per record fastq file" do
|
50
|
+
describe "#each_record" do
|
51
|
+
context "with a gzipped file" do
|
52
|
+
before(:each) do
|
53
|
+
@fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz"
|
54
|
+
end
|
55
|
+
|
56
|
+
it_behaves_like "any FastqFile"
|
57
|
+
|
58
|
+
it "closes the GzipReader" do
|
59
|
+
expect(f_handle).to be_closed
|
60
|
+
end
|
61
|
+
|
62
|
+
it "returns GzipReader object" do
|
63
|
+
expect(f_handle).to be_an_instance_of Zlib::GzipReader
|
64
|
+
end
|
42
65
|
end
|
43
66
|
|
44
|
-
|
45
|
-
|
46
|
-
|
67
|
+
context "with a non-gzipped file" do
|
68
|
+
before(:each) do
|
69
|
+
@fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq"
|
70
|
+
end
|
71
|
+
|
72
|
+
it_behaves_like "any FastqFile"
|
73
|
+
|
74
|
+
it "doesn't close the FastqFile (approx regular file behavior)" do
|
75
|
+
expect(f_handle).not_to be_closed
|
76
|
+
end
|
77
|
+
|
78
|
+
it "returns FastqFile object" do
|
79
|
+
expect(f_handle).to be_an_instance_of FastqFile
|
80
|
+
end
|
47
81
|
end
|
48
82
|
end
|
49
|
-
end
|
83
|
+
end
|
50
84
|
end
|
85
|
+
|
data/spec/lib/quality_spec.rb
CHANGED
data/spec/lib/sequence_spec.rb
CHANGED
data/spec/spec_helper.rb
CHANGED
data/test_files/benchmark.rb
CHANGED
Binary file
|
Binary file
|
metadata
CHANGED
@@ -1,93 +1,94 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: parse_fasta
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.
|
4
|
+
version: 1.5.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ryan Moore
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2015-01-08 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
|
-
- -
|
17
|
+
- - ~>
|
18
18
|
- !ruby/object:Gem::Version
|
19
19
|
version: '1.6'
|
20
20
|
type: :development
|
21
21
|
prerelease: false
|
22
22
|
version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
|
-
- -
|
24
|
+
- - ~>
|
25
25
|
- !ruby/object:Gem::Version
|
26
26
|
version: '1.6'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: rake
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- -
|
31
|
+
- - ~>
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: '10.3'
|
34
34
|
type: :development
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- -
|
38
|
+
- - ~>
|
39
39
|
- !ruby/object:Gem::Version
|
40
40
|
version: '10.3'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
42
|
name: rspec
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- -
|
45
|
+
- - ~>
|
46
46
|
- !ruby/object:Gem::Version
|
47
47
|
version: '2.14'
|
48
48
|
type: :development
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- -
|
52
|
+
- - ~>
|
53
53
|
- !ruby/object:Gem::Version
|
54
54
|
version: '2.14'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
|
name: bio
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- -
|
59
|
+
- - ~>
|
60
60
|
- !ruby/object:Gem::Version
|
61
61
|
version: '1.4'
|
62
62
|
type: :development
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- -
|
66
|
+
- - ~>
|
67
67
|
- !ruby/object:Gem::Version
|
68
68
|
version: '1.4'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: yard
|
71
71
|
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
|
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
|
-
description:
|
83
|
+
description: Provides nice, programmatic access to fasta and fastq files, as well
|
84
|
+
as providing Sequence and Quality helper classes. No need for BioRuby ;)
|
84
85
|
email:
|
85
86
|
- moorer@udel.edu
|
86
87
|
executables: []
|
87
88
|
extensions: []
|
88
89
|
extra_rdoc_files: []
|
89
90
|
files:
|
90
|
-
-
|
91
|
+
- .gitignore
|
91
92
|
- COPYING
|
92
93
|
- Gemfile
|
93
94
|
- README.md
|
@@ -106,10 +107,12 @@ files:
|
|
106
107
|
- spec/spec_helper.rb
|
107
108
|
- test_files/benchmark.rb
|
108
109
|
- test_files/test.fa
|
110
|
+
- test_files/test.fa.gz
|
109
111
|
- test_files/test.fq
|
112
|
+
- test_files/test.fq.gz
|
110
113
|
homepage: https://github.com/mooreryan/parse_fasta
|
111
114
|
licenses:
|
112
|
-
- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
115
|
+
- ! 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
113
116
|
metadata: {}
|
114
117
|
post_install_message:
|
115
118
|
rdoc_options: []
|
@@ -117,12 +120,12 @@ require_paths:
|
|
117
120
|
- lib
|
118
121
|
required_ruby_version: !ruby/object:Gem::Requirement
|
119
122
|
requirements:
|
120
|
-
- -
|
123
|
+
- - ! '>='
|
121
124
|
- !ruby/object:Gem::Version
|
122
125
|
version: 1.9.3
|
123
126
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
124
127
|
requirements:
|
125
|
-
- -
|
128
|
+
- - ! '>='
|
126
129
|
- !ruby/object:Gem::Version
|
127
130
|
version: '0'
|
128
131
|
requirements: []
|
@@ -130,7 +133,7 @@ rubyforge_project:
|
|
130
133
|
rubygems_version: 2.2.2
|
131
134
|
signing_key:
|
132
135
|
specification_version: 4
|
133
|
-
summary: Easy-peasy parsing of fasta files
|
136
|
+
summary: Easy-peasy parsing of fasta & fastq files!
|
134
137
|
test_files:
|
135
138
|
- spec/lib/fasta_file_spec.rb
|
136
139
|
- spec/lib/fastq_file_spec.rb
|