old_contents: #!/usr/bin/python
  #
  # Copyright (c) 2013 Mikkel Schubert <MSchubert@snm.ku.dk>
  #
  # 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.
  #
  import os
  import sys
  
  from pypeline.common.formats.msa import \
       MSA
  
  # Minimum fraction of bases that must be covered across all sequences
  _FRAC_BASES_COVERED = 0.8
  # Exclude the following sequence(s) when calculating covered bases
  _EXCLUDE_SAMPLES = frozenset(("Pi_nucl",))
  
  
  def _is_sufficently_covered(filepath):
      msa = MSA.from_file(filepath)
      if msa.seqlen() % 3:
          return False
  
      filtered_msa = msa.exclude(_EXCLUDE_SAMPLES)
  
      total_bases_not_covered = 0
      for fasta_record in filtered_msa:
          total_bases_not_covered += fasta_record.sequence.upper().count("N")
          total_bases_not_covered += fasta_record.sequence.count("-")
  
      frac_covered = (1.0 - total_bases_not_covered / float(len(filtered_msa) * filtered_msa.seqlen()))
      return frac_covered >= _FRAC_BASES_COVERED
  
  
  def main(argv):
      for root_dir in argv:
          for filename in os.listdir(root_dir):
              if filename.endswith(".afa"):
                  if _is_sufficently_covered(os.path.join(root_dir, filename)):
                      sequence_name, _ = filename.rsplit(".", 1)
                      print(sequence_name)
  
  
  if __name__ == '__main__':
      sys.exit(main(sys.argv[1:]))
  
new_contents: #!/usr/bin/python
  #
  # Copyright (c) 2013 Mikkel Schubert <MSchubert@snm.ku.dk>
  #
  # 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.
  #
  import os
  import sys
  import optparse
  
  from pypeline.common.formats.msa import \
       MSA
  
  def _is_sufficently_covered(filepath, min_coverage):
      msa = MSA.from_file(filepath)
      if msa.seqlen() % 3:
          return False
  
      total_bases_not_covered = 0
      for fasta_record in msa:
          total_bases_not_covered += fasta_record.sequence.upper().count("N")
          total_bases_not_covered += fasta_record.sequence.count("-")
  
      total_bases = float(len(msa) * msa.seqlen())
      frac_covered = 1.0 - total_bases_not_covered / total_bases
      return frac_covered >= min_coverage
  
  
  def main(argv):
      usage = "%prog [options] <PATH>"
      parser = optparse.OptionParser(usage=usage)
      parser.add_option("--min-coverage", default=0.8, type=float,
                        help="Minimum fraction of called bases in a MSA "
                             "[%default]")
  
      config, args = parser.parse_args(argv)
      if not args:
          parser.print_usage()
          return 1
  
      for root_dir in args:
          for filename in os.listdir(root_dir):
              if filename.endswith(".afa"):
                  fpath = os.path.join(root_dir, filename)
                  if _is_sufficently_covered(fpath, config.min_coverage):
                      sequence_name, _ = filename.rsplit(".", 1)
                      print(sequence_name)
  
  
  if __name__ == '__main__':
      sys.exit(main(sys.argv[1:]))
  
subject: Make min. coverage settable.