parse_fasta 2.4.2 → 2.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c235357c072f2b4042b7723dd0c3eb686d5fc60d
-  data.tar.gz: 7f1d7ba7d306774fe35b79f9ec6f773265e7c93e
+  metadata.gz: b58d57b0b3d32e90276f0a95e1bede38e0573439
+  data.tar.gz: 6577ae5b5793f164526b24c2f748a9d782150653
 SHA512:
-  metadata.gz: b3ab4bc141fdd4ed995d9931ecee923e2a81bf07ade851275f9315fe2df09b94c09d6af372bf3b229caedba618c488fac77554b3b02f60ccfbb2e5f901030cbd
-  data.tar.gz: 8d7bee5a8f0cf74db20616165dd0d00a4caa44eec7701e1a4a48ddf6349a6906aa05033307de01b05af8eb5b2fb5e96d7818058c744527ce5ec6cf68a7f1c6d8
+  metadata.gz: c4d717b98e4f8263b9e233bbf398cc09813a34c22dd5899fc4281909869f10776f3298412d546e9546acb423747b5e065d636e1ebbcdb3cb2e3d20bdc5bf2530
+  data.tar.gz: 222bb97de866d13b3e8eeac9208f0f3c838e6e00f8833962bae299de59045b7a9c2a9f58f4a95b81777a1fe0161c4646322dfb0d69e214ed4a7218d7bcfe60f0

data/.gitignore

@@ -24,3 +24,6 @@ mkmf.log
 .idea
 time.html
 big_test_files
+
+rake_?
+ruby_rake_?

data/.travis.yml

@@ -7,12 +7,41 @@ rvm:
   - 2.3
   - 2.4
   - 2.5
-  
+  - ruby-head
+  - jruby-head
+
+jdk:
+  - oraclejdk8
+  - oraclejdk9
+
+matrix:
+  exclude:
+    - rvm: 2.1
+      jdk: oraclejdk8
+    - rvm: 2.1
+      jdk: oraclejdk9
+    - rvm: 2.2
+      jdk: oraclejdk8
+    - rvm: 2.2
+      jdk: oraclejdk9
+    - rvm: 2.3
+      jdk: oraclejdk8
+    - rvm: 2.3
+      jdk: oraclejdk9
+    - rvm: 2.4
+      jdk: oraclejdk8
+    - rvm: 2.4
+      jdk: oraclejdk9
+    - rvm: 2.5
+      jdk: oraclejdk8
+    - rvm: 2.5
+      jdk: oraclejdk9
+
 script: 'bundle exec rake'
 
 notifications:
   email:
     recipients:
       - moorer@udel.edu
-    on_failure: change
-    on_success: never
+    on_failure: always
+    on_success: always

data/README.md

@@ -19,6 +19,10 @@ And then execute:
 Or install it yourself as:
 
     $ gem install parse_fasta
+    
+### JRuby ###
+
+If you want to use `ParseFasta` with JRuby, make sure to use version >= 2.5.    
 
 ## Overview ##
 

data/lib/parse_fasta/seq_file.rb

@@ -209,6 +209,8 @@ module ParseFasta
       line_reader
     end
 
+    # Get the first char of the file whether it is gzip'd or not.  No
+    # need to rewind the stream afterwards.
     def get_first_char fname
       if File.exists? fname
         begin
@@ -217,8 +219,10 @@ module ParseFasta
           f = File.open fname
         end
 
+
         begin
-          first_char = f.each_char.peek[0]
+          first_char = f.each.peek[0]
+
           return first_char
         ensure
           f.close

data/lib/parse_fasta/version.rb

@@ -1,3 +1,3 @@
 module ParseFasta
-  VERSION = "2.4.2"
+  VERSION = "2.5.0"
 end

data/parse_fasta.gemspec

@@ -1,34 +1,32 @@
 # coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
+lib = File.expand_path("../lib", __FILE__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'parse_fasta/version'
+require "parse_fasta/version"
 
 Gem::Specification.new do |spec|
-  spec.name          = "parse_fasta"
-  spec.version       = ParseFasta::VERSION
-  spec.authors       = ["Ryan Moore"]
-  spec.email         = ["moorer@udel.edu"]
-  spec.summary       = %q{Easy-peasy parsing of fasta & fastq files!}
-  spec.description   =
-    "Provides nice, programmatic access to fasta " +
-    "and fastq files, as well as providing Sequence and Quality " +
-    "helper classes. No need for BioRuby ;)"
-  spec.homepage      = "https://github.com/mooreryan/parse_fasta"
-  spec.license       = "GPLv3: http://www.gnu.org/licenses/gpl.txt"
+  spec.name        = "parse_fasta"
+  spec.version     = ParseFasta::VERSION
+  spec.authors     = ["Ryan Moore"]
+  spec.email       = ["moorer@udel.edu"]
+  spec.summary     = %q{Easy-peasy parsing of fasta & fastq files!}
+  spec.description = <<-EOF
+Provides nice, programmatic access to fasta and fastq files, as well as providing Sequence and Quality helper classes. No need for BioRuby ;)
+  EOF
+  spec.homepage = "https://github.com/mooreryan/parse_fasta"
+  spec.license  = "MIT"
 
   spec.files         = `git ls-files -z`.split("\x0")
-  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.executables   = spec.files.grep(%r{^bin/}) {|f| File.basename(f)}
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
   spec.required_ruby_version = ">= 2.1"
 
-  spec.add_development_dependency "bundler", "~> 1.6"
-  spec.add_development_dependency "rake", "~> 10.3"
-  spec.add_development_dependency "rspec", "~> 2.14"
+  spec.add_development_dependency "bundler", "~> 1.16", ">= 1.16.1"
+  spec.add_development_dependency "rake", "~> 12.3", ">= 12.3.1"
+  spec.add_development_dependency "rspec", "~> 3.7"
   spec.add_development_dependency "bio", "~> 1.4"
-  spec.add_development_dependency "yard", "~> 0.8"
-  spec.add_development_dependency "rdiscount"
-  spec.add_development_dependency "coveralls", "~> 0.7"
+  spec.add_development_dependency "yard", "~> 0.9.12"
+  spec.add_development_dependency "coveralls", "~> 0.8.21"
   spec.add_development_dependency "benchmark-ips", "~> 2.7", ">= 2.7.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 2.4.2
+  version: 2.5.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-17 00:00:00.000000000 Z
+date: 2018-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -16,42 +16,54 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.16'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.16.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.16'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.16.1
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '12.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.3.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '12.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.3.1
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '3.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '3.7'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
@@ -72,42 +84,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: 0.9.12
   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'
+        version: 0.9.12
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.7'
+        version: 0.8.21
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.7'
+        version: 0.8.21
 - !ruby/object:Gem::Dependency
   name: benchmark-ips
   requirement: !ruby/object:Gem::Requirement
@@ -128,8 +126,10 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.7.2
-description: Provides nice, programmatic access to fasta and fastq files, as well
+description: 'Provides nice, programmatic access to fasta and fastq files, as well
   as providing Sequence and Quality helper classes. No need for BioRuby ;)
+
+'
 email:
 - moorer@udel.edu
 executables:
@@ -142,8 +142,6 @@ files:
 - ".gitignore"
 - ".rspec"
 - ".travis.yml"
-- ".yardopts"
-- CHANGELOG.md
 - Gemfile
 - LICENSE
 - README.md
@@ -182,7 +180,7 @@ files:
 - spec/test_files/with_rec_sep_in_seq.fa
 homepage: https://github.com/mooreryan/parse_fasta
 licenses:
-- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
+- MIT
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -200,7 +198,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: Easy-peasy parsing of fasta & fastq files!
@@ -228,4 +226,3 @@ test_files:
 - spec/test_files/seqs.fq.gz
 - spec/test_files/test.rb
 - spec/test_files/with_rec_sep_in_seq.fa
-has_rdoc: 

data/.yardopts

@@ -1 +0,0 @@
---markup-provider rdiscount

data/CHANGELOG.md

@@ -1,194 +0,0 @@
-## Versions ##
-
-### 2.3.0 ###
-
-Allow parsing of fastA files with `>` characters in the sequence with the `check_fasta_seq: false` option.
-
-### 2.2.0 ###
-
-Add `id` attribute to `Record`.
-
-### 2.1.1 ###
-
-Speed up `Record.new`
-
-### 2.1.0 ###
-
-Add `#to_s`, `#to_fasta`, and `#to_fastq` to `Record`.
-
-### 2.0.0 ###
-
-A weird feature of `Zlib::GzipReader` made it so that if a gzipped file was created like this.
-
-```bash
-gzip -c a.fa > z.fa.gz
-gzip -c b.fa >> z.fa.gz
-```
-
-Then the gzip reader would only read the lines from `a.fa` without some fiddling around. Since this was a pretty low level thing, I just decided to make a bunch of under the hood changes that I've been meaning to get to.
-
-#### Other things
-
-- Everything is namespaced under `ParseFasta` module
-- Removed `FastaFile` and `FastqFile` classes, `SeqFile` only remains
-- Removed `Sequence` and `Quality` classes. These might get put back in at some point, but I almost never used them anyway
-- `SeqFile#each_record` yields a `Record` object so you can use the same code to parse fastA and fastQ files
-- Other stuff that I'm forgetting!
-
-
-### 1.9.2 ###
-
-Speed up fastA `each_record` and `each_record_fast`.
-
-### 1.9.1 ###
-
-Speed up fastQ `each_record` and `each_record_fast`. Courtesy of
-[Matthew Ralston](https://github.com/MatthewRalston).
-
-### 1.9.0 ###
-
-Added "fast" versions of `each_record` methods
-(`each_record_fast`). Basically, they return sequences and quality
-strings as Ruby `Sring` objects instead of aa `Sequence` or `Quality`
-objects. Also, if the sequence or quality string has spaces, they will
-be retained. If this is a problem, use the original `each_record`
-methods.
-
-### 1.8.2 ###
-
-Speed up `FastqFile#each_record`.
-
-### 1.8.1 ###
-
-An error will be raised if a fasta file has a `>` in the
-sequence. Sometimes files are not terminated with a newline
-character. If this is the case, then catting two fasta files will
-smush the first header of the second file right in with the last
-sequence of the first file. This is bad, raise an error! ;)
-
-Example
-
-    >seq1
-    ACTG>seq2
-    ACTG
-    >seq3
-    ACTG
-
-This will raise `ParseFasta::SequenceFormatError`.
-
-Also, headers with lots of `>` within are fine now.
-
-### 1.8 ###
-
-Add `Sequence#rev_comp`. It can handle IUPAC characters. Since
-`parse_fasta` doesn't check whether the seq is AA or NA, if called on
-an amino acid string, things will get weird as it will complement the
-IUPAC characters in the AA string and leave others.
-
-### 1.7.2 ###
-
-Strip spaces (not all whitespace) from `Sequence` and `Quality` strings.
-
-Some alignment fastas have spaces for easier reading. Strip these
-out. For consistency, also strips spaces from `Quality` strings. If
-there are spaces that don't match in the quality and sequence in a
-fastQ file, then things will get messed up in the FastQ file. FastQ
-shouldn't have spaces though.
-
-### 1.7 ###
-
-Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
-
-### 1.6.2 ###
-
-`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
-that don't begin with a `>`.
-
-### 1.6.1 ###
-
-Better internal handling of empty sequences -- instead of raising
-errors, pass empty sequences.
-
-### 1.6 ###
-
-Added `SeqFile` class, which accepts either fastA or fastQ files. It
-uses FastaFile and FastqFile internally. You can use this class if you
-want your scripts to accept either fastA or fastQ files.
-
-If you need the description and quality string, you should use
-FastqFile instead.
-
-### 1.5 ###
-
-Now accepts gzipped files. Huzzah!
-
-### 1.4 ###
-
-Added methods:
-
-    Sequence.base_counts
-	Sequence.base_frequencies
-
-### 1.3 ###
-
-Add additional functionality to `each_record` method.
-
-#### Info ####
-
-I often like to use the fasta format for other things like so
-
-	>fruits
-	pineapple
-	pear
-	peach
-	>veggies
-	peppers
-	parsnip
-	peas
-
-rather than having this in a two column file like this
-
-	fruit,pineapple
-	fruit,pear
-	fruit,peach
-	veggie,peppers
-	veggie,parsnip
-	veggie,peas
-
-So I added functionality to `each_record` to keep each line a record
-separate in an array. Here's an example using the above file.
-
-    info = []
-	FastaFile.open(f, 'r').each_record(1) do |header, lines|
-	  info << [header, lines]
-	end
-
-Then info will contain the following arrays
-
-	['fruits', ['pineapple', 'pear', 'peach']],
-	['veggies', ['peppers', 'parsnip', 'peas']]
-
-### 1.2 ###
-
-Added `mean_qual` method to the `Quality` class.
-
-### 1.1.2 ###
-
-Dropped Ruby requirement to 1.9.3
-
-(Note, if you want to build the docs with yard and you're using
-Ruby 1.9.3, you may have to install the redcarpet gem.)
-
-### 1.1 ###
-
-Added: Fastq and Quality classes
-
-### 1.0 ###
-
-Added: Fasta and Sequence classes
-
-Removed: File monkey patch
-
-### 0.0.5 ###
-
-Last version with File monkey patch.