parse_fasta 1.9.2 → 2.0.0

data/spec/lib/fasta_file_spec.rb

@@ -1,212 +0,0 @@
-# Copyright 2014, 2015 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/>.
-
-require 'spec_helper'
-
-describe FastaFile do
-  describe "::open" do
-    context "when input is bogus" do
-      it "raises a ParseFasta::DataFormatError with message" do
-        fname = "#{File.dirname(__FILE__)}/../../test_files/bogus.txt"
-
-        expect { FastaFile.open(fname).each_record do |h, s|
-            puts [h, s].join ' '
-          end
-        }.to raise_error ParseFasta::DataFormatError
-      end
-    end
-
-    let(:fasta) { "#{File.dirname(__FILE__)}/../../test_files/test.fa" }
-
-    it "takes all the wacky args like IO.open" do
-      expect {
-        FastaFile.open(fasta, mode: 'r', cr_newline: true)
-      }.not_to raise_error
-    end
-
-    it "returns a FastaFile" do
-      expect(FastaFile.open(fasta)).to be_a FastaFile
-    end
-  end
-
-  describe "#to_hash" do
-    let(:records) { Helpers::RECORDS_MAP }
-    let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz" }
-    let(:fasta) { FastaFile.open(fname) }
-
-    context "with badly catted fasta" do
-      it "raises ParseFasta::SequenceFormatError" do
-        fname = "#{File.dirname(__FILE__)}/../../test_files/bad.fa"
-
-        expect { FastaFile.open(fname).to_hash }.
-          to raise_error ParseFasta::SequenceFormatError
-      end
-    end
-
-    it "reads the records into a hash: header as key and seq as val" do
-      expect(fasta.to_hash).to eq records
-    end
-
-    it "passes the values as Sequence objects" do
-      expect(
-        fasta.to_hash.values.all? { |val| val.instance_of? Sequence }
-      ).to eq true
-    end
-  end
-
-  describe "#each_record" do
-    let(:records) { Helpers::RECORDS }
-
-    let(:truthy_records) { Helpers::TRUTHY_RECORDS }
-    let(:f_handle) { FastaFile.open(@fname).each_record { |s| } }
-
-    context "with badly catted fasta" do
-      it "raises ParseFasta::SequenceFormatError" do
-        fname = "#{File.dirname(__FILE__)}/../../test_files/bad.fa"
-
-        expect { FastaFile.open(fname).each_record {} }.
-          to raise_error ParseFasta::SequenceFormatError
-      end
-    end
-
-    shared_examples_for "any FastaFile" do
-      context "with no arguments" do
-        it "yields proper header and sequence for each record" do
-          expect { |b|
-            FastaFile.open(@fname).each_record(&b)
-          }.to yield_successive_args(*records)
-        end
-
-        it "yields the sequence as a Sequence class" do
-          FastaFile.open(@fname).each_record do |_, seq|
-            expect(seq).to be_an_instance_of Sequence
-          end
-        end
-      end
-
-      context "with a truthy argument" do
-        it "yields proper header and sequence for each record" do
-          expect { |b|
-            FastaFile.open(@fname).each_record(1, &b)
-          }.to yield_successive_args(*truthy_records)
-        end
-
-        it "yields the sequence as a Sequence class" do
-          FastaFile.open(@fname).each_record(1) do |_, seq|
-            all_Sequences = seq.map { |s| s.instance_of?(Sequence) }.all?
-            expect(all_Sequences).to be true
-          end
-        end
-
-      end
-    end
-
-    context "with a gzipped file" do
-      before(:each) do
-        @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz"
-      end
-
-      it_behaves_like "any FastaFile"
-
-      it "closes the GzipReader" do
-        expect(f_handle).to be_closed
-      end
-
-      it "returns GzipReader object" do
-        expect(f_handle).to be_an_instance_of Zlib::GzipReader
-      end
-    end
-
-    context "with a non-gzipped file" do
-      before(:each) do
-        @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa"
-      end
-
-      it_behaves_like "any FastaFile"
-
-      it "doesn't close the FastqFile (approx regular file behavior)" do
-        expect(f_handle).not_to be_closed
-      end
-
-      it "returns FastaFile object" do
-        expect(f_handle).to be_an_instance_of FastaFile
-      end
-    end
-  end
-
-  describe "#each_record_fast" do
-    let(:records) { Helpers::RECORDS_FAST }
-
-    let(:f_handle) { FastaFile.open(@fname).each_record_fast { |s| } }
-
-    context "with badly catted fasta" do
-      it "raises ParseFasta::SequenceFormatError" do
-        fname = "#{File.dirname(__FILE__)}/../../test_files/bad.fa"
-
-        expect { FastaFile.open(fname).each_record_fast {} }.
-          to raise_error ParseFasta::SequenceFormatError
-      end
-    end
-
-    shared_examples_for "any FastaFile" do
-      it "yields proper header and sequence for each record" do
-        expect { |b|
-          FastaFile.open(@fname).each_record_fast(&b)
-        }.to yield_successive_args(*records)
-      end
-
-      it "yields the sequence as a String class" do
-        FastaFile.open(@fname).each_record_fast do |_, seq|
-          expect(seq).to be_an_instance_of String
-        end
-      end
-    end
-
-    context "with a gzipped file" do
-      before(:each) do
-        @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa.gz"
-      end
-
-      it_behaves_like "any FastaFile"
-
-      it "closes the GzipReader" do
-        expect(f_handle).to be_closed
-      end
-
-      it "returns GzipReader object" do
-        expect(f_handle).to be_an_instance_of Zlib::GzipReader
-      end
-    end
-
-    context "with a non-gzipped file" do
-      before(:each) do
-        @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fa"
-      end
-
-      it_behaves_like "any FastaFile"
-
-      it "doesn't close the FastqFile (approx regular file behavior)" do
-        expect(f_handle).not_to be_closed
-      end
-
-      it "returns FastaFile object" do
-        expect(f_handle).to be_an_instance_of FastaFile
-      end
-    end
-  end
-end

data/spec/lib/fastq_file_spec.rb

@@ -1,143 +0,0 @@
-# Copyright 2014, 2015 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/>.
-
-require 'spec_helper'
-
-describe FastqFile do
-  let(:records) {
-    [["seq1", "AACCTTGG", "", ")#3gTqN8"],
-     ["seq2 apples", "ACTG", "seq2 apples", "*ujM"]]
-  }
-
-  let(:records_fast) {
-    [["seq1", "AA CC TT GG", "", ")# 3g Tq N8"],
-     ["seq2 apples", "ACTG", "seq2 apples", "*ujM"]]
-  }
-
-  let(:f_handle) { FastqFile.open(@fname).each_record { |s| } }
-
-
-  shared_examples_for "any FastqFile" do
-    it "yields proper header, sequence, description, and quality" do
-      expect { |b|
-        FastqFile.open(@fname).each_record(&b)
-      }.to yield_successive_args(records[0], records[1])
-    end
-
-    it "yields the sequence as a Sequence class" do
-      FastqFile.open(@fname).each_record do |_, seq, _, _|
-        expect(seq).to be_an_instance_of Sequence
-      end
-    end
-
-    it "yields the quality as a Quality class" do
-      FastqFile.open(@fname).each_record do |_, _, _, qual|
-        expect(qual).to be_an_instance_of Quality
-      end
-    end
-  end
-
-  describe "#each_record_fast" do
-    before(:each) do
-      @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz"
-    end
-
-    it "yields proper header, sequence, description, and quality" do
-      expect { |b|
-        FastqFile.open(@fname).each_record_fast(&b)
-      }.to yield_successive_args(records_fast[0], records_fast[1])
-    end
-
-    it "yields all params as String" do
-      FastqFile.open(@fname).each_record_fast do |h, s, d, q|
-        expect(h).to be_an_instance_of String
-        expect(s).to be_an_instance_of String
-        expect(d).to be_an_instance_of String
-        expect(q).to be_an_instance_of String
-      end
-    end
-  end
-
-  describe "#to_hash" do
-    let(:records) {
-      { "seq1" => { head: "seq1",
-                    seq: "AACCTTGG",
-                    desc: "",
-                    qual: ")#3gTqN8" },
-        "seq2 apples" => { head: "seq2 apples",
-                           seq: "ACTG",
-                           desc: "seq2 apples",
-                           qual: "*ujM" }
-      }
-    }
-    let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz" }
-    let(:fastq) { FastqFile.open(fname) }
-
-    it "reads the records into a hash: header as key and seq as val" do
-      expect(fastq.to_hash).to eq records
-    end
-
-    it "passes the seqs as Sequence objects" do
-      expect(
-        fastq.to_hash.values.all? { |val| val[:seq].instance_of? Sequence }
-      ).to eq true
-    end
-
-    it "passes the quals as Quality objects" do
-      expect(
-        fastq.to_hash.values.all? { |val| val[:qual].instance_of? Quality }
-      ).to eq true
-    end
-  end
-
-  context "with a 4 line per record fastq file" do
-    describe "#each_record" do
-      context "with a gzipped file" do
-        before(:each) do
-          @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz"
-        end
-
-        it_behaves_like "any FastqFile"
-
-        it "closes the GzipReader" do
-          expect(f_handle).to be_closed
-        end
-
-        it "returns GzipReader object" do
-          expect(f_handle).to be_an_instance_of Zlib::GzipReader
-        end
-      end
-
-      context "with a non-gzipped file" do
-        before(:each) do
-          @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq"
-        end
-
-        it_behaves_like "any FastqFile"
-
-        it "doesn't close the FastqFile (approx regular file behavior)" do
-          expect(f_handle).not_to be_closed
-        end
-
-        it "returns FastqFile object" do
-          expect(f_handle).to be_an_instance_of FastqFile
-        end
-      end
-    end
-  end
-end

data/spec/lib/quality_spec.rb

@@ -1,51 +0,0 @@
-# Copyright 2014, 2015 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/>.
-
-require 'spec_helper'
-require 'bio'
-
-describe Quality do
-  let(:qual_string) { qual_string = Quality.new('ab%63:K') }
-  let(:bioruby_qual_scores) do
-    Bio::Fastq.new("@seq1\nACTGACT\n+\n#{qual_string}").quality_scores
-  end
-
-  describe "::new" do
-    it "removes any spaces in the quality string" do
-      q = "   ab #   :m, !    "
-      q_no_spaces = "ab#:m,!"
-      expect(Quality.new(q)).to eq q_no_spaces
-    end
-  end
-
-  describe "#qual_scores" do
-    context "with illumina style quality scores" do
-      it "returns an array of quality scores" do
-        expect(qual_string.qual_scores).to eq bioruby_qual_scores
-      end
-    end
-  end
-
-  describe "#mean_qual" do
-    it "returns the mean quality for the quality string" do
-      len = qual_string.length.to_f
-      mean_quality = qual_string.qual_scores.reduce(:+) / len
-      expect(qual_string.mean_qual).to eq mean_quality
-    end
-  end
-end