parse_fasta 2.0.0 → 2.0.1

checksums.yaml

@@ -1,15 +1,7 @@
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data/.travis.yml

@@ -2,11 +2,10 @@ language: ruby
 cache: bundler
 
 rvm:
-  - 1.9.3
   - 2.0
   - 2.1
-  - 2.2.0
-  - 2.2.2
+  - 2.2
+  - 2.3
 
 script: 'bundle exec rake'
 

data/lib/parse_fasta/seq_file.rb

@@ -18,39 +18,6 @@
 
 require "zlib"
 
-def get_first_char fname
-  if File.exists? fname
-    begin
-      f = Zlib::GzipReader.open fname
-    rescue Zlib::GzipFile::Error
-      f = File.open fname
-    ensure
-      # f.close
-    end
-
-    first_char = f.each_char.peek[0]
-    f.close
-    return first_char
-  else
-    raise ParseFasta::Error::FileNotFoundError,
-          "No such file or directory -- #{fname}"
-  end
-end
-
-def check_file fname
-  first_char = get_first_char fname
-
-  if first_char == ">"
-    :fasta
-  elsif first_char == "@"
-    :fastq
-  else
-    raise ParseFasta::Error::DataFormatError,
-          "The file does not look like fastA or fastQ " +
-              "-- #{fname}"
-  end
-end
-
 module ParseFasta
   class SeqFile
     # @!attribute type
@@ -250,5 +217,39 @@ module ParseFasta
 
       line_reader
     end
+
+    def get_first_char fname
+      if File.exists? fname
+        begin
+          f = Zlib::GzipReader.open fname
+        rescue Zlib::GzipFile::Error
+          f = File.open fname
+        end
+
+        begin
+          first_char = f.each_char.peek[0]
+          return first_char
+        ensure
+          f.close
+        end
+      else
+        raise ParseFasta::Error::FileNotFoundError,
+              "No such file or directory -- #{fname}"
+      end
+    end
+
+    def check_file fname
+      first_char = get_first_char fname
+
+      if first_char == ">"
+        :fasta
+      elsif first_char == "@"
+        :fastq
+      else
+        raise ParseFasta::Error::DataFormatError,
+              "The file does not look like fastA or fastQ " +
+                  "-- #{fname}"
+      end
+    end
   end
 end

data/lib/parse_fasta/version.rb

@@ -17,5 +17,5 @@
 # along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
 
 module ParseFasta
-  VERSION = "2.0.0"
+  VERSION = "2.0.1"
 end

data/parse_fasta.gemspec

@@ -21,7 +21,7 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.required_ruby_version = ">= 1.9.3"
+  spec.required_ruby_version = ">= 2"
 
   spec.add_development_dependency "bundler", "~> 1.6"
   spec.add_development_dependency "rake", "~> 10.3"

data/spec/test_files/test.rb

@@ -0,0 +1,71 @@
+require "parse_fasta"
+
+fasta_records =
+  [ParseFasta::Record.new(header: "empty seq at beginning",
+              seq: ""),
+   ParseFasta::Record.new(header: "seq1 is fun",
+              seq: "AACTGGNNN"),
+   ParseFasta::Record.new(header: "seq2",
+              seq: "AATCCTGNNN"),
+   ParseFasta::Record.new(header: "empty seq 1",
+              seq: ""),
+   ParseFasta::Record.new(header: "empty seq 2",
+              seq: ""),
+   ParseFasta::Record.new(header: "seq3",
+              seq: "yyyyyyyyyyyyyyyNNN"),
+   ParseFasta::Record.new(header: "seq 4 > has many '>' in header",
+              seq: "ACTGactg"),
+   ParseFasta::Record.new(header: "empty seq at end",
+              seq: "")]
+
+fastq_records =
+  [ParseFasta::Record.new(header: "seq1",
+              seq: "AA CC TT GG",
+              desc: "",
+              qual: ")# 3g Tq N8"),
+   ParseFasta::Record.new(header: "seq2 @pples",
+              seq:    "ACTG",
+              desc:   "seq2 +pples",
+              qual:   "*ujM")]
+
+
+line_endings_fastq_records =
+  [ParseFasta::Record.new(header: "apple", seq: "ACTG", desc: "", qual: "IIII"),
+   ParseFasta::Record.new(header: "pie",   seq: "AACC", desc: "", qual: "BBBB"),]
+
+line_endings_fasta_records =
+  [ParseFasta::Record.new(header: "apple", seq: "ACTG"),
+   ParseFasta::Record.new(header: "pie",   seq: "AACC"),]
+
+def check fname, expected_records
+  STDERR.puts "\nReading #{fname}"
+  recs = []
+  ParseFasta::SeqFile.open(File.join File.dirname(__FILE__), fname).each_record do |rec|
+    p [rec.header, rec.seq, rec.desc, rec.qual]
+    recs << rec
+  end
+  STDERR.puts "Good? #{recs == expected_records}"
+
+  $results << (recs == expected_records)
+end
+
+$results = []
+
+check "seqs.fa",    fasta_records
+check "seqs.fa.gz", fasta_records
+check "seqs.fq",    fastq_records
+check "seqs.fq.gz", fastq_records
+
+check "cr.fa",       line_endings_fasta_records
+check "cr.fa.gz",    line_endings_fasta_records
+check "cr_nl.fa",    line_endings_fasta_records
+check "cr_nl.fa.gz", line_endings_fasta_records
+
+check "cr.fq",       line_endings_fastq_records
+check "cr.fq.gz",    line_endings_fastq_records
+check "cr_nl.fq",    line_endings_fastq_records
+check "cr_nl.fq.gz", line_endings_fastq_records
+
+if $results.all? { |res| res }
+  STDERR.puts "\nAll Good!\n\n"
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
 platform: ruby
 authors:
 - Ryan Moore
@@ -14,98 +14,98 @@ dependencies:
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.6'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.14'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
 - !ruby/object:Gem::Dependency
   name: rdiscount
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
 description: Provides nice, programmatic access to fasta and fastq files, as well
@@ -118,11 +118,11 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- .coveralls.yml
-- .gitignore
-- .rspec
-- .travis.yml
-- .yardopts
+- ".coveralls.yml"
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- ".yardopts"
 - CHANGELOG.md
 - COPYING
 - Gemfile
@@ -156,9 +156,10 @@ files:
 - spec/test_files/seqs.fa.gz
 - spec/test_files/seqs.fq
 - spec/test_files/seqs.fq.gz
+- spec/test_files/test.rb
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
-- ! 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
+- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -166,17 +167,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.9.3
+      version: '2'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Easy-peasy parsing of fasta & fastq files!
@@ -201,4 +202,5 @@ test_files:
 - spec/test_files/seqs.fa.gz
 - spec/test_files/seqs.fq
 - spec/test_files/seqs.fq.gz
+- spec/test_files/test.rb
 has_rdoc: