Tests of FastaReader ok

.editorconfig

+root = true
+
+[*.cr]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true

.gitignore

+/docs/
+/lib/
+/bin/
+/.shards/
+*.dwarf
+
+# Libraries don't need dependency lock
+# Dependencies will be locked in applications that use them
+/shard.lock

.travis.yml

+language: crystal
+
+# Uncomment the following if you'd like Travis to run specs and check code formatting
+# script:
+#   - crystal spec
+#   - crystal tool format --check

LICENSE

+The MIT License (MIT)
+
+Copyright (c) 2020 your-name-here
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

+# fasta_reader
+
+TODO: Write a description here
+
+## Installation
+
+1. Add the dependency to your `shard.yml`:
+
+   ```yaml
+   dependencies:
+     fasta_reader:
+       github: your-github-user/fasta_reader
+   ```
+
+2. Run `shards install`
+
+## Usage
+
+```crystal
+require "fasta_reader"
+```
+
+TODO: Write usage instructions here
+
+## Development
+
+TODO: Write development instructions here
+
+## Contributing
+
+1. Fork it (<https://github.com/your-github-user/fasta_reader/fork>)
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request
+
+## Contributors
+
+- [your-name-here](https://github.com/your-github-user) - creator and maintainer

shard.yml

+name: fasta_reader
+version: 0.1.0
+
+authors:
+  - your-name-here <your-email-here>
+
+crystal: 0.35.1
+
+license: MIT

spec/fasta_reader_spec.cr

+require "./spec_helper"
+include FastaReader
+
+describe FastaReader do
+  # TODO: Write tests
+
+  records = [] of FastaRecord
+
+  FastaReader.each_fasta("spec/test.fasta") do |rec|
+    records << rec
+  end
+
+  it "has the right number of records" do
+    records.size.should eq 3
+  end
+  it "has the right header for record 1" do
+    records[0][:hdr].should eq "ID_01"
+  end
+  it "has the right sequence for record 1" do
+    records[0][:seq].should eq "atgatgatgcttcttctt"
+  end
+  it "has the right header for record 2" do
+    records[1][:hdr].should eq "ID 02"
+  end
+  it "has the right sequence for record 2" do
+    records[1][:seq].should eq "cgatcgacgatcgatgcacgatgaacctacgagcartcgagcatcagagcagcatcgagcagctacgagatt"
+  end
+  it "has the right header for record 3" do
+    records[2][:hdr].should eq "XPQ_LATCH|Latimeria chalumnae unknown protein" 
+  end
+  it "has the right sequence for record 3" do
+    records[2][:seq].should eq "MERTHSNSGDKTSTVSLDVLSRHSHSSVNSTSDHTSASKRSVHDRFHSTCSCM"
+  end
+end

spec/spec_helper.cr

+require "spec"
+require "../src/fasta_reader"

spec/test.fasta

+>ID_01
+atgatgatg
+cttcttctt
+>ID 02
+cgatcgacgatcgatgcacgatga
+acctacgagcartcgagcatcaga
+gcagcatcgagcagctacgagatt
+>XPQ_LATCH|Latimeria chalumnae unknown protein
+MERTHSNSGDKTSTVSLDV
+LSRHSHSSVNSTSDHTS
+ASKRSVHDRFHSTCSCM

src/fasta_reader.cr

+# TODO: Write documentation for `FastaReader`
+module FastaReader
+  VERSION = "0.1.0"
+
+  extend self
+
+  alias FastaRecord = NamedTuple(hdr: String, seq: String)
+
+  def each_fasta(fasta_fname : String, &block : FastaRecord -> Nil)
+    File.open(fasta_fname) do |fasta|
+      header = nil
+      sequence = ""
+      fasta.each_line do |line|
+        first_char = line[0, 1]
+        case first_char
+        when ">"
+          if header
+            rec = {hdr: header[1..], seq: sequence}
+            yield rec
+          end
+          header = line
+          sequence = ""
+        when /[a-zA-Z-]/
+          sequence = sequence.not_nil! + line
+        else
+          raise "Unexpected residue character \"#{first_char}\""
+        end
+      end
+      # yield the last entry
+      if header
+        rec = {hdr: header[1..], seq: sequence}
+        yield rec
+      end
+    end
+  end
+
+end

src/seq_readers.cr

+
+module FastaReader
+  extend self
+
+  alias FastaRecord = NamedTuple{hdr: String, seq: String}
+
+  def each_fasta(fasta_fname : String, &block : Entry -> Nil)
+    File.open(fasta_fname) do |fasta|
+      header = nil
+      sequence = ""
+      fasta.each_line do |line|
+        first_char = line[0, 1]
+        case first_char
+        when ">"
+          if header
+            rec = {hdr: header, seq: sequence}
+            yield rec
+          end
+          header = line
+          sequence = ""
+        when /[a-zA-Z-]/
+          sequence = sequence.not_nil! + line
+        else
+          raise "Unexpected residue character \"#{first_char}\""
+        end
+      end
+      # yield the last entry
+      if header
+        rec = {hdr: header, seq: sequence}
+        yield rec
+      end
+    end
+  end
+
+end