parse_fasta 1.8.1 → 1.8.2

checksums.yaml

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data/README.md

@@ -66,14 +66,11 @@ Read fasta file into a hash.
 
 ## Versions ##
 
-### 1.8 ###
+### 1.8.2 ###
 
-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.
+Speed up `FastqFile#each_record`.
 
-#### 1.8.1 ####
+### 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
@@ -93,12 +90,14 @@ This will raise `ParseFasta::SequenceFormatError`.
 
 Also, headers with lots of `>` within are fine now.
 
+### 1.8 ###
 
-### 1.7 ###
-
-Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
+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 ####
+### 1.7.2 ###
 
 Strip spaces (not all whitespace) from `Sequence` and `Quality` strings.
 
@@ -108,24 +107,28 @@ 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.
 
-### 1.6 ###
+### 1.7 ###
 
-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.
+Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
 
-If you need the description and quality string, you should use
-FastqFile instead.
+### 1.6.2 ###
+
+`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
+that don't begin with a `>`.
 
-#### 1.6.1 ####
+### 1.6.1 ###
 
 Better internal handling of empty sequences -- instead of raising
 errors, pass empty sequences.
 
-#### 1.6.2 ####
+### 1.6 ###
 
-`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
-that don't begin with a `>`.
+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 ###
 
@@ -204,17 +207,16 @@ Last version with File monkey patch.
 
 ## Benchmark ##
 
-Perhaps this isn't exactly fair since `BioRuby` is a big module with
-lots of features and error checking, whereas `parse_fasta` is meant to
-be lightweight and easy to use for my own research. Oh well ;)
+**NOTE**: These benchmarks are against an older version of
+  `parse_fasta`.
+
+Some quick and dirty benchmarks against `BioRuby`.
 
 ### FastaFile#each_record ###
 
-You're probably wondering...How does it compare to BioRuby in some
-super accurate benchmarking tests? Lucky for you, I calculated
-sequence length for each fasta record with both the `each_record`
-method from this gem and using the `FastaFormat` class from
-BioRuby. You can see the test script in `benchmark.rb`.
+Calculating sequence length length for each fasta record with both the
+`each_record` method from this gem and using the `FastaFormat` class
+from BioRuby. You can see the test script in `benchmark.rb`.
 
 The test file contained 2,009,897 illumina reads and the file size
 was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
@@ -255,20 +257,10 @@ test 2 was 4,000,000 and test 3 was 8,000,000 bases.
 
 Nice!
 
-Troll: "But Ryan, when will you find the GC of an 8,000,000 base
-sequence?"
+Troll: "When will you find the GC of an 8,000,000 base sequence?"
 
 Me: "Step off, troll!"
 
-## Test suite & docs ##
-
-For a good time, you could clone this repo and run the test suite with
-rspec! Or if you just don't trust that it works like it should. The
-specs probably need a little clean up...so fork it and clean it up ;)
-
-Same with the docs. Clone the repo and build them yourself with `yard`
-if you are in need of some excitement.
-
 ## Notes ##
 
 Only the `SeqFile` class actually checks to make sure that you passed

data/lib/parse_fasta/fastq_file.rb

@@ -80,11 +80,11 @@ class FastqFile < File
 
       case count % 4
       when 0
-        header = line.sub(/^@/, '')
+        header = line[1..-1]
       when 1
         sequence = Sequence.new(line)
       when 2
-        description = line.sub(/^\+/, '')
+        description = line[1..-1]
       when 3
         quality = Quality.new(line)
         yield(header, sequence, description, quality)

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 = "1.8.1"
+  VERSION = "1.8.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.8.1
+  version: 1.8.2
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-11 00:00:00.000000000 Z
+date: 2016-04-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler