<commit_before>class Transdecoder < Formula
  desc "Identifies candidate coding regions within transcript sequences"
  homepage "https://transdecoder.github.io/"
  url "https://github.com/TransDecoder/TransDecoder/archive/v3.0.0.tar.gz"
  sha256 "b5a1ad48c0df64bb539709e523418bbe197d0342bd2fae40e035234946bcaeb6"
  head "https://github.com/TransDecoder/TransDecoder.git"
  # tag "bioinformatics"

  head "https://github.com/TransDecoder/TransDecoder.git"

  bottle do
    cellar :any
    sha256 "559044bf89f298ede284e3a9f72ef0fc7bd6c912e2b5ee753ceade016370d704" => :yosemite
    sha256 "fae619c6f41eec60f5bf1bd76af2b110253be8fee275c7610c3bf7ac80873b02" => :mavericks
    sha256 "549db77a17285d8a616d64e1e6b9baf21e3beb9e424d6427dfce9af43737c30a" => :mountain_lion
    sha256 "36447454b2c6504477ef1335989cad531efaa4c2032646e6d8356b440625cbaf" => :x86_64_linux
  end

  depends_on "cd-hit"

  def install
    # Remove the cd-hit source code
    rm_rf "transdecoder_plugins"

    prefix.install Dir["*"]
    bin.install_symlink "../TransDecoder.LongOrfs", "../TransDecoder.Predict"
  end

  test do
    assert_match "USAGE", shell_output("#{bin}/TransDecoder.LongOrfs 2>&1", 1)
    assert_match "USAGE", shell_output("#{bin}/TransDecoder.Predict 2>&1", 1)
  end
end
<commit_msg>transdecoder: update 3.0.0 bottle.<commit_after>class Transdecoder < Formula
  desc "Identifies candidate coding regions within transcript sequences"
  homepage "https://transdecoder.github.io/"
  url "https://github.com/TransDecoder/TransDecoder/archive/v3.0.0.tar.gz"
  sha256 "b5a1ad48c0df64bb539709e523418bbe197d0342bd2fae40e035234946bcaeb6"
  head "https://github.com/TransDecoder/TransDecoder.git"
  # tag "bioinformatics"

  head "https://github.com/TransDecoder/TransDecoder.git"

  bottle do
    cellar :any_skip_relocation
    sha256 "ce741f3518c5cb58affd3b81448c15e744ebe94aebdd5643b48862cf05834eb2" => :el_capitan
    sha256 "4a50568376ef0523f282e83df50e022d967c96973cbbefc39facab97c5203f85" => :yosemite
    sha256 "eff88daefa4b2d0478e396c96f6106d6930cde4a096efad125a2cd544cab1c9c" => :mavericks
  end

  depends_on "cd-hit"

  def install
    # Remove the cd-hit source code
    rm_rf "transdecoder_plugins"

    prefix.install Dir["*"]
    bin.install_symlink "../TransDecoder.LongOrfs", "../TransDecoder.Predict"
  end

  test do
    assert_match "USAGE", shell_output("#{bin}/TransDecoder.LongOrfs 2>&1", 1)
    assert_match "USAGE", shell_output("#{bin}/TransDecoder.Predict 2>&1", 1)
  end
end

{'fraction_non_alphanumeric': 0.1033373542420587, 'fraction_numerical': 0.16083634901487737, 'mean_word_length': 5.235588972431078, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 14, 'https://': 8, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7438284', 'n_tokens_mistral': 1191, 'n_tokens_neox': 966, 'n_words': 142}