parse_fasta 1.9.2 → 2.0.0

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data/.gitignore

@@ -21,3 +21,4 @@ tmp
 *.a
 mkmf.log
 .ruby-*
+.idea

data/.rspec

@@ -0,0 +1,2 @@
+--format documentation
+--color

data/CHANGELOG.md

@@ -0,0 +1,178 @@
+## Versions ##
+
+### 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.

data/README.md

@@ -1,4 +1,4 @@
-# parse_fasta #
+# ParseFasta #
 
 [![Gem Version](https://badge.fury.io/rb/parse_fasta.svg)](http://badge.fury.io/rb/parse_fasta) [![Build Status](https://travis-ci.org/mooreryan/parse_fasta.svg?branch=master)](https://travis-ci.org/mooreryan/parse_fasta) [![Coverage Status](https://coveralls.io/repos/mooreryan/parse_fasta/badge.svg)](https://coveralls.io/r/mooreryan/parse_fasta)
 
@@ -8,7 +8,9 @@ So you want to parse a fasta file...
 
 Add this line to your application's Gemfile:
 
-    gem 'parse_fasta'
+```ruby
+gem 'parse_fasta'
+```
 
 And then execute:
 
@@ -20,9 +22,7 @@ Or install it yourself as:
 
 ## Overview ##
 
-Provides nice, programmatic access to fasta and fastq files, as well
-as providing Sequence and Quality helper classes. It's more
-lightweight than BioRuby. And more fun! ;)
+Provides nice, programmatic access to fasta and fastq files. It's faster and more lightweight than BioRuby. And more fun!
 
 ## Documentation ##
 
@@ -32,213 +32,40 @@ for the full api documentation.
 
 ## Usage ##
 
-Some examples...
-
-A little script to print header and length of each record.
-
-	require 'parse_fasta'
-
-	FastaFile.open(ARGV[0]).each_record do |header, sequence|
-	  puts [header, sequence.length].join("\t")
-	end
-
-And here, a script to calculate GC content:
-
-	FastaFile.open(ARGV[0]).each_record do |header, sequence|
-	  puts [header, sequence.gc].join("\t")
-	end
-
-Now we can parse fastq files as well!
-
-	FastqFile.open(ARGV[0]).each_record do |head, seq, desc, qual|
-	  puts [header, qual.qual_scores.join(',')].join("\t")
-	end
-
-What if you don't care if the input is a fastA or a fastQ? No problem!
-
-	SeqFile.open(ARGV[0]).each_record do |head, seq|
-	  puts [header, seq].join "\t"
-	end
-
-Read fasta file into a hash.
-
-    seqs = FastaFile.open(ARGV[0]).to_hash
-
-## Versions ##
-
-### 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.
-
-## Benchmark ##
-
-Some quick and dirty benchmarks against `BioRuby`.
-
-### FastaFile#each_record ###
-
-You can see the test script in `benchmark.rb`.
-
-                           user     system      total        real
-    parse_fasta        1.920000   0.160000   2.080000 (  2.145932)
-    parse_fasta fast   1.210000   0.160000   1.370000 (  1.377770)
-    bioruby            4.330000   0.290000   4.620000 (  4.655567)
-
-Hot dog! It's faster :)
-
-## Notes ##
-
-Only the `SeqFile` class actually checks to make sure that you passed
-in a "proper" fastA or fastQ file, so watch out.
+Here are some examples of using ParseFasta. Don't forget to `require "parse_fasta"` at the top of your program!
+
+Print header and length of each record.
+
+```ruby
+ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
+  puts [rec.header, rec.seq.length].join "\t"
+end
+```
+
+You can parse fastQ files in exatcly the same way.
+
+```ruby
+ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
+  printf "Header: %s, Sequence: %s, Description: %s, Quality: %s\n",
+	     rec.header,
+	     rec.seq,
+	     rec.desc,
+	     rec.qual
+end
+```
+
+The `Record#desc` and `Record#qual` will be `nil` if the file you are parsing is a fastA file.
+
+```ruby
+ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
+  if rec.qual
+    puts "@#{rec.header}"
+    puts rec.seq
+    puts "+#{rec.desc}"
+    puts rec.qual
+  else
+    puts ">#{rec.header}"
+    puts rec.sequence
+  end  
+end
+```

data/Rakefile

@@ -1,8 +1,6 @@
 require "bundler/gem_tasks"
 require "rspec/core/rake_task"
 
-RSpec::Core::RakeTask.new
-
-task default: :spec
-task test: :spec
+RSpec::Core::RakeTask.new(:spec)
 
+task :default => :spec

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "parse_fasta"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/parse_fasta/error.rb

@@ -0,0 +1,39 @@
+# Copyright 2014 - 2016 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of parse_fasta.
+#
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+module ParseFasta
+  # Contains the Error classes that ParseFasta API will raise
+  module Error
+
+    # All ParseFasta errors inherit from ParseFastaError
+    class ParseFastaError < StandardError
+    end
+
+    # Raised when the input file doesn't look like fastA or fastQ
+    class DataFormatError < ParseFastaError
+    end
+
+    # Raised when the file is not found
+    class FileNotFoundError < ParseFastaError
+    end
+
+    # Raised when fastA sequences have a '>' in them
+    class SequenceFormatError < ParseFastaError
+    end
+  end
+end

data/lib/parse_fasta/record.rb

@@ -0,0 +1,88 @@
+# Copyright 2014 - 2016 Ryan Moore
+# Contact: moorer@udel.edu
+#
+# This file is part of parse_fasta.
+#
+# parse_fasta is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# parse_fasta is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
+
+module ParseFasta
+  class Record
+
+    # @!attribute header
+    #   @return [String] the full header of the record without the '>'
+    #     or '@'
+    # @!attribute seq
+    #   @return [String] the sequence of the record
+    # @!attribute desc
+    #   @return [String or Nil] if the record is from a fastA file, it
+    #     is nil; else, the description line of the fastQ record
+    # @!attribute qual
+    #   @return [String or Nil] if the record is from a fastA file, it
+    #     is nil; else, the quality string of the fastQ record
+    attr_accessor :header, :seq, :desc, :qual
+
+    # The constructor takes keyword args.
+    #
+    # @example Init a new Record object for a fastA record
+    #   Record.new header: "apple", seq: "actg"
+    # @example Init a new Record object for a fastQ record
+    #   Record.new header: "apple", seq: "actd", desc: "", qual: "IIII"
+    #
+    # @param header [String] the header of the record
+    # @param seq [String] the sequence of the record
+    # @param desc [String] the description line of a fastQ record
+    # @param qual [String] the quality string of a fastQ record
+    #
+    # @raise [SequenceFormatError] if a fastA sequence has a '>'
+    #   character in it
+    def initialize args = {}
+      @header = args.fetch :header
+
+      @desc = args.fetch :desc, nil
+      @qual = args.fetch :qual, nil
+
+      @qual.gsub!(/\s+/, "") if @qual
+
+      seq = args.fetch(:seq).gsub(/\s+/, "")
+
+      if @qual # is fastQ
+        @seq = seq
+      else # is fastA
+        @seq = check_fasta_seq(seq)
+      end
+    end
+
+    # Compare attrs of this rec with another
+    #
+    # @param rec [Record] a Record object to compare with
+    #
+    # @return [Bool] true or false
+    def == rec
+      self.header == rec.header && self.seq == rec.seq &&
+          self.desc == rec.desc && self.qual == rec.qual
+    end
+
+    private
+
+    def check_fasta_seq seq
+      if seq.match ">"
+        raise ParseFasta::Error::SequenceFormatError,
+              "A sequence contained a '>' character " +
+                  "(the fastA file record separator)"
+      else
+        seq
+      end
+    end
+  end
+end