text: # Copyright 2007-2011 by Peter Cock.  All rights reserved.
  #
  # This code is part of the Biopython distribution and governed by its
  # license.  Please see the LICENSE file that should have been included
  # as part of this package..
  
  """Bio.SeqIO support for the "genbank" and "embl" file formats.
  
  You are expected to use this module via the Bio.SeqIO functions.
  Note that internally this module calls Bio.GenBank to do the actual
  parsing of GenBank, EMBL and IMGT files.
  
  See also:
  
  International Nucleotide Sequence Database Collaboration
  http://www.insdc.org/
  
  GenBank
  http://www.ncbi.nlm.nih.gov/Genbank/
  
  EMBL Nucleotide Sequence Database
  http://www.ebi.ac.uk/embl/
  
  DDBJ (DNA Data Bank of Japan)
  http://www.ddbj.nig.ac.jp/
  
  IMGT (use a variant of EMBL format with longer feature indents)
  http://imgt.cines.fr/download/LIGM-DB/userman_doc.html
  http://imgt.cines.fr/download/LIGM-DB/ftable_doc.html
  http://www.ebi.ac.uk/imgt/hla/docs/manual.html
  
  """
  
  from __future__ import print_function
  
  import warnings
  from Bio import BiopythonWarning
  
  from Bio.Seq import UnknownSeq
  from Bio.GenBank.Scanner import GenBankScanner, EmblScanner, _ImgtScanner
  from Bio import Alphabet
  from Bio.SeqIO.Interfaces import SequentialSequenceWriter
  from Bio import SeqFeature
  
  from Bio._py3k import _is_int_or_long
  from Bio._py3k import basestring
  
  __docformat__ = "restructuredtext en"
  
  # NOTE
  # ====
  # The "brains" for parsing GenBank, EMBL and IMGT files (and any
  # other flat file variants from the INSDC in future) is in
  # Bio.GenBank.Scanner (plus the _FeatureConsumer in Bio.GenBank)
  # However, all the writing code is in this file.
  
  
  def GenBankIterator(handle):
      """Breaks up a Genbank file into SeqRecord objects.
  
      Every section from the LOCUS line to the terminating // becomes
      a single SeqRecord with associated annotation and features.
  
      Note that for genomes or chromosomes, there is typically only
      one record.
  
      This gets called internally by Bio.SeqIO for the GenBank file format:
  
      >>> from Bio import SeqIO
      >>> for record in SeqIO.parse("GenBank/cor6_6.gb", "gb"):
      ...     print(record.id)
      ...
      X55053.1
      X62281.1
      M81224.1
      AJ237582.1
      L31939.1
      AF297471.1
  
      Equivalently,
  
      >>> with open("GenBank/cor6_6.gb") as handle:
      ...     for record in GenBankIterator(handle):
      ...         print(record.id)
      ...
      X55053.1
      X62281.1
      M81224.1
      AJ237582.1
      L31939.1
      AF297471.1
  
      """
      # This calls a generator function:
      return GenBankScanner(debug=0).parse_records(handle)
  
  
  def EmblIterator(handle):
      """Breaks up an EMBL file into SeqRecord objects.
  
      Every section from the LOCUS line to the terminating // becomes
      a single SeqRecord with associated annotation and features.
  
      Note that for genomes or chromosomes, there is typically only
      one record.
  
      This gets called internally by Bio.SeqIO for the EMBL file format:
  
      >>> from Bio import SeqIO
      >>> for record in SeqIO.parse("EMBL/epo_prt_selection.embl", "embl"):
      ...     print(record.id)
      ...
      A00022.1
      A00028.1
      A00031.1
      A00034.1
      A00060.1
      A00071.1
      A00072.1
      A00078.1
      CQ797900.1
  
      Equivalently,
  
      >>> with open("EMBL/epo_prt_selection.embl") as handle:
      ...     for record in EmblIterator(handle):
      ...         print(record.id)
      ...
      A00022.1
      A00028.1
      A00031.1
      A00034.1
      A00060.1
      A00071.1
      A00072.1
      A00078.1
      CQ797900.1
  
      """
      # This calls a generator function:
      return EmblScanner(debug=0).parse_records(handle)
  
  
  def ImgtIterator(handle):
      """Breaks up an IMGT file into SeqRecord objects.
  
      Every section from the LOCUS line to the terminating // becomes
      a single SeqRecord with associated annotation and features.
  
      Note that for genomes or chromosomes, there is typically only
      one record."""
      # This calls a generator function:
      return _ImgtScanner(debug=0).parse_records(handle)
  
  
  def GenBankCdsFeatureIterator(handle, alphabet=Alphabet.generic_protein):
      """Breaks up a Genbank file into SeqRecord objects for each CDS feature.
  
      Every section from the LOCUS line to the terminating // can contain
      many CDS features.  These are returned as with the stated amino acid
      translation sequence (if given).
      """
      # This calls a generator function:
      return GenBankScanner(debug=0).parse_cds_features(handle, alphabet)
  
  
  def EmblCdsFeatureIterator(handle, alphabet=Alphabet.generic_protein):
      """Breaks up a EMBL file into SeqRecord objects for each CDS feature.
  
      Every section from the LOCUS line to the terminating // can contain
      many CDS features.  These are returned as with the stated amino acid
      translation sequence (if given).
      """
      # This calls a generator function:
      return EmblScanner(debug=0).parse_cds_features(handle, alphabet)
  
  
  def _insdc_feature_position_string(pos, offset=0):
      """Build a GenBank/EMBL position string (PRIVATE).
  
      Use offset=1 to add one to convert a start position from python counting.
      """
      if isinstance(pos, SeqFeature.ExactPosition):
          return "%i" % (pos.position + offset)
      elif isinstance(pos, SeqFeature.WithinPosition):
          return "(%i.%i)" % (pos.position + offset,
                              pos.position + pos.extension + offset)
      elif isinstance(pos, SeqFeature.BetweenPosition):
          return "(%i^%i)" % (pos.position + offset,
                              pos.position + pos.extension + offset)
      elif isinstance(pos, SeqFeature.BeforePosition):
          return "<%i" % (pos.position + offset)
      elif isinstance(pos, SeqFeature.AfterPosition):
          return ">%i" % (pos.position + offset)
      elif isinstance(pos, SeqFeature.OneOfPosition):
          return "one-of(%s)" \
                 % ",".join(_insdc_feature_position_string(p, offset)
                            for p in pos.position_choices)
      elif isinstance(pos, SeqFeature.AbstractPosition):
          raise NotImplementedError("Please report this as a bug in Biopython.")
      else:
          raise ValueError("Expected a SeqFeature position object.")
  
  
  def _insdc_location_string_ignoring_strand_and_subfeatures(location, rec_length):
      if location.ref:
          ref = "%s:" % location.ref
      else:
          ref = ""
      assert not location.ref_db
      if isinstance(location.start, SeqFeature.ExactPosition) \
          and isinstance(location.end, SeqFeature.ExactPosition) \
              and location.start.position == location.end.position:
          # Special case, for 12:12 return 12^13
          # (a zero length slice, meaning the point between two letters)
          if location.end.position == rec_length:
              # Very special case, for a between position at the end of a
              # sequence (used on some circular genomes, Bug 3098) we have
              # N:N so return N^1
              return "%s%i^1" % (ref, rec_length)
          else:
              return "%s%i^%i" % (ref, location.end.position,
                                  location.end.position + 1)
      if isinstance(location.start, SeqFeature.ExactPosition) \
          and isinstance(location.end, SeqFeature.ExactPosition) \
              and location.start.position + 1 == location.end.position:
          # Special case, for 11:12 return 12 rather than 12..12
          # (a length one slice, meaning a single letter)
          return "%s%i" % (ref, location.end.position)
      elif isinstance(location.start, SeqFeature.UnknownPosition) \
              or isinstance(location.end, SeqFeature.UnknownPosition):
          # Special case for features from SwissProt/UniProt files
          if isinstance(location.start, SeqFeature.UnknownPosition) \
                  and isinstance(location.end, SeqFeature.UnknownPosition):
              # warnings.warn("Feature with unknown location", BiopythonWarning)
              # return "?"
              raise ValueError("Feature with unknown location")
          elif isinstance(location.start, SeqFeature.UnknownPosition):
              # Treat the unknown start position as a BeforePosition
              return "%s<%i..%s" \
                  % (ref,
                     location.nofuzzy_end,
                     _insdc_feature_position_string(location.end))
          else:
              # Treat the unknown end position as an AfterPosition
              return "%s%s..>%i" \
                  % (ref,
                     _insdc_feature_position_string(location.start),
                     location.nofuzzy_start)
      else:
          # Typical case, e.g. 12..15 gets mapped to 11:15
          return ref \
              + _insdc_feature_position_string(location.start, +1) \
              + ".." + \
              _insdc_feature_position_string(location.end)
  
  
  def _insdc_location_string(location, rec_length):
      """Build a GenBank/EMBL location from a (Compound) FeatureLocation (PRIVATE).
  
      There is a choice of how to show joins on the reverse complement strand,
      GenBank used "complement(join(1,10),(20,100))" while EMBL used to use
      "join(complement(20,100),complement(1,10))" instead (but appears to have
      now adopted the GenBank convention). Notice that the order of the entries
      is reversed! This function therefore uses the first form. In this situation
      we expect the CompoundFeatureLocation and its parts to all be marked as
      strand == -1, and to be in the order 19:100 then 0:10.
      """
      try:
          parts = location.parts
          # CompoundFeatureLocation
          if location.strand == -1:
              # Special case, put complement outside the join/order/... and reverse order
              return "complement(%s(%s))" % (location.operator,
                     ",".join(_insdc_location_string_ignoring_strand_and_subfeatures(p, rec_length)
                              for p in parts[::-1]))
          else:
              return "%s(%s)" % (location.operator,
                     ",".join(_insdc_location_string(p, rec_length) for p in parts))
      except AttributeError:
          # Simple FeatureLocation
          loc = _insdc_location_string_ignoring_strand_and_subfeatures(location, rec_length)
          if location.strand == -1:
              return "complement(%s)" % loc
          else:
              return loc
  
  
  def _insdc_feature_location_string(feature, rec_length):
      """Build a GenBank/EMBL location string from a SeqFeature (PRIVATE, OBSOLETE).
  
      There is a choice of how to show joins on the reverse complement strand,
      GenBank used "complement(join(1,10),(20,100))" while EMBL used to use
      "join(complement(20,100),complement(1,10))" instead (but appears to have
      now adopted the GenBank convention). Notice that the order of the entries
      is reversed! This function therefore uses the first form. In this situation
      we expect the parent feature and the two children to all be marked as
      strand == -1, and in the order 0:10 then 19:100.
  
      Also need to consider dual-strand examples like these from the Arabidopsis
      thaliana chloroplast NC_000932: join(complement(69611..69724),139856..140650)
      gene ArthCp047, GeneID:844801 or its CDS (protein NP_051038.1 GI:7525057)
      which is further complicated by a splice:
      join(complement(69611..69724),139856..140087,140625..140650)
  
      For this mixed strand feature, the parent SeqFeature should have
      no strand (either 0 or None) while the child features should have either
      strand +1 or -1 as appropriate, and be listed in the order given here.
      """
      # Using private variable to avoid deprecation warning
      if not feature._sub_features:
          # Non-recursive.
          # assert feature.location_operator == "", \
          #       "%s has no subfeatures but location_operator %s" \
          #       % (repr(feature), feature.location_operator)
          location = _insdc_location_string_ignoring_strand_and_subfeatures(
              feature.location, rec_length)
          if feature.strand == -1:
              location = "complement(%s)" % location
          return location
      # As noted above, treat reverse complement strand features carefully:
      if feature.strand == -1:
          for f in feature._sub_features:
              if f.strand != -1:
                  raise ValueError("Inconsistent strands: %r for parent, %r for child"
                                   % (feature.strand, f.strand))
          return "complement(%s(%s))" \
                 % (feature.location_operator,
                    ",".join(_insdc_location_string_ignoring_strand_and_subfeatures(f.location, rec_length)
                             for f in feature._sub_features))
      # if feature.strand == +1:
      #    for f in feature.sub_features:
      #        assert f.strand == +1
      # This covers typical forward strand features, and also an evil mixed strand:
      assert feature.location_operator != ""
      return "%s(%s)" % (feature.location_operator,
                         ",".join(_insdc_feature_location_string(f, rec_length)
                                  for f in feature._sub_features))
  
  
  class _InsdcWriter(SequentialSequenceWriter):
      """Base class for GenBank and EMBL writers (PRIVATE)."""
      MAX_WIDTH = 80
      QUALIFIER_INDENT = 21
      QUALIFIER_INDENT_STR = " " * QUALIFIER_INDENT
      QUALIFIER_INDENT_TMP = "     %s                "  # 21 if %s is empty
      FTQUAL_NO_QUOTE = ("anticodon", "citation", "codon_start", "compare",
                         "direction", "estimated_length", "mod_base", "number",
                         "rpt_type", "rpt_unit_range", "tag_peptide",
                         "transl_except", "transl_table")
  
      def _write_feature_qualifier(self, key, value=None, quote=None):
          if value is None:
              # Value-less entry like /pseudo
              self.handle.write("%s/%s\n" % (self.QUALIFIER_INDENT_STR, key))
              return
          # Quick hack with no line wrapping, may be useful for testing:
          # self.handle.write('%s/%s="%s"\n' % (self.QUALIFIER_INDENT_STR, key, value))
          if quote is None:
              # Try to mimic unwritten rules about when quotes can be left out:
              if _is_int_or_long(value) or key in self.FTQUAL_NO_QUOTE:
                  quote = False
              else:
                  quote = True
          if quote:
              line = '%s/%s="%s"' % (self.QUALIFIER_INDENT_STR, key, value)
          else:
              line = '%s/%s=%s' % (self.QUALIFIER_INDENT_STR, key, value)
          if len(line) <= self.MAX_WIDTH:
              self.handle.write(line + "\n")
              return
          while line.lstrip():
              if len(line) <= self.MAX_WIDTH:
                  self.handle.write(line + "\n")
                  return
              # Insert line break...
              for index in range(min(len(line) - 1, self.MAX_WIDTH),
                                 self.QUALIFIER_INDENT + 1, -1):
                  if line[index] == " ":
                      break
              if line[index] != " ":
                  # No nice place to break...
                  index = self.MAX_WIDTH
              assert index <= self.MAX_WIDTH
              self.handle.write(line[:index] + "\n")
              line = self.QUALIFIER_INDENT_STR + line[index:].lstrip()
  
      def _wrap_location(self, location):
          """Split a feature location into lines (break at commas)."""
          # TODO - Rewrite this not to recurse!
          length = self.MAX_WIDTH - self.QUALIFIER_INDENT
          if len(location) <= length:
              return location
          index = location[:length].rfind(",")
          if index == -1:
              # No good place to split (!)
              warnings.warn("Couldn't split location:\n%s" % location,
                            BiopythonWarning)
              return location
          return location[:index + 1] + "\n" + \
              self.QUALIFIER_INDENT_STR + \
              self._wrap_location(location[index + 1:])
  
      def _write_feature(self, feature, record_length):
          """Write a single SeqFeature object to features table."""
          assert feature.type, feature
          location = _insdc_location_string(feature.location, record_length)
          f_type = feature.type.replace(" ", "_")
          line = (self.QUALIFIER_INDENT_TMP % f_type)[:self.QUALIFIER_INDENT] \
                 + self._wrap_location(location) + "\n"
          self.handle.write(line)
          # Now the qualifiers...
          for key in sorted(feature.qualifiers.keys()):
              values = feature.qualifiers[key]
              if isinstance(values, (list, tuple)):
                  for value in values:
                      self._write_feature_qualifier(key, value)
              else:
                  # String, int, etc - or None for a /pseudo tpy entry
                  self._write_feature_qualifier(key, values)
  
      def _get_annotation_str(self, record, key, default=".", just_first=False):
          """Get an annotation dictionary entry (as a string).
  
          Some entries are lists, in which case if just_first=True the first entry
          is returned.  If just_first=False (default) this verifies there is only
          one entry before returning it."""
          try:
              answer = record.annotations[key]
          except KeyError:
              return default
          if isinstance(answer, list):
              if not just_first:
                  assert len(answer) == 1
              return str(answer[0])
          else:
              return str(answer)
  
      def _split_multi_line(self, text, max_len):
          """Returns a list of strings.
  
          Any single words which are too long get returned as a whole line
          (e.g. URLs) without an exception or warning.
          """
          # TODO - Do the line spliting while preserving white space?
          text = text.strip()
          if len(text) <= max_len:
              return [text]
  
          words = text.split()
          text = ""
          while words and len(text) + 1 + len(words[0]) <= max_len:
              text += " " + words.pop(0)
              text = text.strip()
          # assert len(text) <= max_len
          answer = [text]
          while words:
              text = words.pop(0)
              while words and len(text) + 1 + len(words[0]) <= max_len:
                  text += " " + words.pop(0)
                  text = text.strip()
              # assert len(text) <= max_len
              answer.append(text)
          assert not words
          return answer
  
      def _split_contig(self, record, max_len):
          """Returns a list of strings, splits on commas."""
          # TODO - Merge this with _write_multi_line method?
          # It would need the addition of the comma splitting logic...
          # are there any other cases where that would be sensible?
          contig = record.annotations.get("contig", "")
          if isinstance(contig, (list, tuple)):
              contig = "".join(contig)
          contig = self.clean(contig)
          answer = []
          while contig:
              if len(contig) > max_len:
                  # Split lines at the commas
                  pos = contig[:max_len - 1].rfind(",")
                  if pos == -1:
                      raise ValueError("Could not break up CONTIG")
                  text, contig = contig[:pos + 1], contig[pos + 1:]
              else:
                  text, contig = contig, ""
              answer.append(text)
          return answer
  
  
  class GenBankWriter(_InsdcWriter):
      HEADER_WIDTH = 12
      QUALIFIER_INDENT = 21
  
      def _write_single_line(self, tag, text):
          """Used in the 'header' of each GenBank record."""
          assert len(tag) < self.HEADER_WIDTH
          if len(text) > self.MAX_WIDTH - self.HEADER_WIDTH:
              warnings.warn("Annotation %r too long for %r line" % (text, tag),
                            BiopythonWarning)
          self.handle.write("%s%s\n" % (tag.ljust(self.HEADER_WIDTH),
                                        text.replace("\n", " ")))
  
      def _write_multi_line(self, tag, text):
          """Used in the 'header' of each GenBank record."""
          # TODO - Do the line spliting while preserving white space?
          max_len = self.MAX_WIDTH - self.HEADER_WIDTH
          lines = self._split_multi_line(text, max_len)
          self._write_single_line(tag, lines[0])
          for line in lines[1:]:
              self._write_single_line("", line)
  
      def _write_multi_entries(self, tag, text_list):
          # used for DBLINK and any similar later line types.
          # If the list of strings is empty, nothing is written.
          for i, text in enumerate(text_list):
              if i == 0:
                  self._write_single_line(tag, text)
              else:
                  self._write_single_line("", text)
  
      def _get_date(self, record):
          default = "01-JAN-1980"
          try:
              date = record.annotations["date"]
          except KeyError:
              return default
          # Cope with a list of one string:
          if isinstance(date, list) and len(date) == 1:
              date = date[0]
          # TODO - allow a Python date object
          if not isinstance(date, basestring) or len(date) != 11 \
              or date[2] != "-" or date[6] != "-" \
              or not date[:2].isdigit() or not date[7:].isdigit() \
              or int(date[:2]) > 31 \
              or date[3:6] not in ["JAN", "FEB", "MAR", "APR", "MAY", "JUN",
                                   "JUL", "AUG", "SEP", "OCT", "NOV", "DEC"]:
              # TODO - Check is a valid date (e.g. not 31 Feb)
              return default
          return date
  
      def _get_data_division(self, record):
          try:
              division = record.annotations["data_file_division"]
          except KeyError:
              division = "UNK"
          if division in ["PRI", "ROD", "MAM", "VRT", "INV", "PLN", "BCT",
                          "VRL", "PHG", "SYN", "UNA", "EST", "PAT", "STS",
                          "GSS", "HTG", "HTC", "ENV", "CON"]:
              # Good, already GenBank style
              #    PRI - primate sequences
              #    ROD - rodent sequences
              #    MAM - other mammalian sequences
              #    VRT - other vertebrate sequences
              #    INV - invertebrate sequences
              #    PLN - plant, fungal, and algal sequences
              #    BCT - bacterial sequences [plus archea]
              #    VRL - viral sequences
              #    PHG - bacteriophage sequences
              #    SYN - synthetic sequences
              #    UNA - unannotated sequences
              #    EST - EST sequences (expressed sequence tags)
              #    PAT - patent sequences
              #    STS - STS sequences (sequence tagged sites)
              #    GSS - GSS sequences (genome survey sequences)
              #    HTG - HTGS sequences (high throughput genomic sequences)
              #    HTC - HTC sequences (high throughput cDNA sequences)
              #    ENV - Environmental sampling sequences
              #    CON - Constructed sequences
              #
              # (plus UNK for unknown)
              pass
          else:
              # See if this is in EMBL style:
              #    Division                 Code
              #    -----------------        ----
              #    Bacteriophage            PHG - common
              #    Environmental Sample     ENV - common
              #    Fungal                   FUN - map to PLN (plants + fungal)
              #    Human                    HUM - map to PRI (primates)
              #    Invertebrate             INV - common
              #    Other Mammal             MAM - common
              #    Other Vertebrate         VRT - common
              #    Mus musculus             MUS - map to ROD (rodent)
              #    Plant                    PLN - common
              #    Prokaryote               PRO - map to BCT (poor name)
              #    Other Rodent             ROD - common
              #    Synthetic                SYN - common
              #    Transgenic               TGN - ??? map to SYN ???
              #    Unclassified             UNC - map to UNK
              #    Viral                    VRL - common
              #
              # (plus XXX for submiting which we can map to UNK)
              embl_to_gbk = {"FUN": "PLN",
                             "HUM": "PRI",
                             "MUS": "ROD",
                             "PRO": "BCT",
                             "UNC": "UNK",
                             "XXX": "UNK",
                             }
              try:
                  division = embl_to_gbk[division]
              except KeyError:
                  division = "UNK"
          assert len(division) == 3
          return division
  
      def _write_the_first_line(self, record):
          """Write the LOCUS line."""
  
          locus = record.name
          if not locus or locus == "<unknown name>":
              locus = record.id
          if not locus or locus == "<unknown id>":
              locus = self._get_annotation_str(
                  record, "accession", just_first=True)
          if len(locus) > 16:
              raise ValueError("Locus identifier %r is too long" % str(locus))
  
          if len(record) > 99999999999:
              # Currently GenBank only officially support up to 350000, but
              # the length field can take eleven digits
              raise ValueError("Sequence too long!")
  
          # Get the base alphabet (underneath any Gapped or StopCodon encoding)
          a = Alphabet._get_base_alphabet(record.seq.alphabet)
          if not isinstance(a, Alphabet.Alphabet):
              raise TypeError("Invalid alphabet")
          elif isinstance(a, Alphabet.ProteinAlphabet):
              units = "aa"
          elif isinstance(a, Alphabet.NucleotideAlphabet):
              units = "bp"
          else:
              # Must be something like NucleotideAlphabet or
              # just the generic Alphabet (default for fasta files)
              raise ValueError("Need a Nucleotide or Protein alphabet")
  
          # Get the molecule type
          # TODO - record this explicitly in the parser?
          if isinstance(a, Alphabet.ProteinAlphabet):
              mol_type = ""
          elif isinstance(a, Alphabet.DNAAlphabet):
              mol_type = "DNA"
          elif isinstance(a, Alphabet.RNAAlphabet):
              mol_type = "RNA"
          else:
              # Must be something like NucleotideAlphabet or
              # just the generic Alphabet (default for fasta files)
              raise ValueError("Need a DNA, RNA or Protein alphabet")
  
          division = self._get_data_division(record)
  
          assert len(units) == 2
          assert len(division) == 3
          # TODO - date
          # TODO - mol_type
          line = "LOCUS       %s %s %s    %s           %s %s\n" \
              % (locus.ljust(16),
                 str(len(record)).rjust(11),
                 units,
                 mol_type.ljust(6),
                 division,
                 self._get_date(record))
          assert len(line) == 79 + 1, repr(line)  # plus one for new line
  
          assert line[12:28].rstrip() == locus, \
              'LOCUS line does not contain the locus at the expected position:\n' + line
          assert line[28:29] == " "
          assert line[29:40].lstrip() == str(len(record)), \
              'LOCUS line does not contain the length at the expected position:\n' + line
  
          # Tests copied from Bio.GenBank.Scanner
          assert line[40:44] in [' bp ', ' aa '], \
              'LOCUS line does not contain size units at expected position:\n' + \
              line
          assert line[44:47] in ['   ', 'ss-', 'ds-', 'ms-'], \
              'LOCUS line does not have valid strand type (Single stranded, ...):\n' + line
          assert line[47:54].strip() == "" \
              or 'DNA' in line[47:54].strip() \
              or 'RNA' in line[47:54].strip(), \
                 'LOCUS line does not contain valid sequence type (DNA, RNA, ...):\n' + line
          assert line[54:55] == ' ', \
              'LOCUS line does not contain space at position 55:\n' + line
          assert line[55:63].strip() in ['', 'linear', 'circular'], \
              'LOCUS line does not contain valid entry (linear, circular, ...):\n' + line
          assert line[63:64] == ' ', \
              'LOCUS line does not contain space at position 64:\n' + line
          assert line[67:68] == ' ', \
              'LOCUS line does not contain space at position 68:\n' + line
          assert line[70:71] == '-', \
              'LOCUS line does not contain - at position 71 in date:\n' + line
          assert line[74:75] == '-', \
              'LOCUS line does not contain - at position 75 in date:\n' + line
  
          self.handle.write(line)
  
      def _write_references(self, record):
          number = 0
          for ref in record.annotations["references"]:
              if not isinstance(ref, SeqFeature.Reference):
                  continue
              number += 1
              data = str(number)
              # TODO - support more complex record reference locations?
              if ref.location and len(ref.location) == 1:
                  a = Alphabet._get_base_alphabet(record.seq.alphabet)
                  if isinstance(a, Alphabet.ProteinAlphabet):
                      units = "residues"
                  else:
                      units = "bases"
                  data += "  (%s %i to %i)" % (units,
                                               ref.location[0].nofuzzy_start + 1,
                                               ref.location[0].nofuzzy_end)
              self._write_single_line("REFERENCE", data)
              if ref.authors:
                  # We store the AUTHORS data as a single string
                  self._write_multi_line("  AUTHORS", ref.authors)
              if ref.consrtm:
                  # We store the consortium as a single string
                  self._write_multi_line("  CONSRTM", ref.consrtm)
              if ref.title:
                  # We store the title as a single string
                  self._write_multi_line("  TITLE", ref.title)
              if ref.journal:
                  # We store this as a single string - holds the journal name,
                  # volume, year, and page numbers of the citation
                  self._write_multi_line("  JOURNAL", ref.journal)
              if ref.medline_id:
                  # This line type is obsolete and was removed from the GenBank
                  # flatfile format in April 2005. Should we write it?
                  # Note this has a two space indent:
                  self._write_multi_line("  MEDLINE", ref.medline_id)
              if ref.pubmed_id:
                  # Note this has a THREE space indent:
                  self._write_multi_line("   PUBMED", ref.pubmed_id)
              if ref.comment:
                  self._write_multi_line("  REMARK", ref.comment)
  
      def _write_comment(self, record):
          # This is a bit complicated due to the range of possible
          # ways people might have done their annotation...
          # Currently the parser uses a single string with newlines.
          # A list of lines is also reasonable.
          # A single (long) string is perhaps the most natural of all.
          # This means we may need to deal with line wrapping.
          comment = record.annotations["comment"]
          if isinstance(comment, basestring):
              lines = comment.split("\n")
          elif isinstance(comment, (list, tuple)):
              lines = comment
          else:
              raise ValueError("Could not understand comment annotation")
          self._write_multi_line("COMMENT", lines[0])
          for line in lines[1:]:
              self._write_multi_line("", line)
  
      def _write_contig(self, record):
          max_len = self.MAX_WIDTH - self.HEADER_WIDTH
          lines = self._split_contig(record, max_len)
          self._write_single_line("CONTIG", lines[0])
          for text in lines[1:]:
              self._write_single_line("", text)
  
      def _write_sequence(self, record):
          # Loosely based on code from Howard Salis
          # TODO - Force lower case?
          LETTERS_PER_LINE = 60
          SEQUENCE_INDENT = 9
  
          if isinstance(record.seq, UnknownSeq):
              # We have already recorded the length, and there is no need
              # to record a long sequence of NNNNNNN...NNN or whatever.
              if "contig" in record.annotations:
                  self._write_contig(record)
              else:
                  self.handle.write("ORIGIN\n")
              return
  
          # Catches sequence being None:
          data = self._get_seq_string(record).lower()
          seq_len = len(data)
          self.handle.write("ORIGIN\n")
          for line_number in range(0, seq_len, LETTERS_PER_LINE):
              self.handle.write(str(line_number + 1).rjust(SEQUENCE_INDENT))
              for words in range(line_number,
                                 min(line_number + LETTERS_PER_LINE, seq_len), 10):
                  self.handle.write(" %s" % data[words:words + 10])
              self.handle.write("\n")
  
      def write_record(self, record):
          """Write a single record to the output file."""
          handle = self.handle
          self._write_the_first_line(record)
  
          accession = self._get_annotation_str(record, "accession",
                                               record.id.split(".", 1)[0],
                                               just_first=True)
          acc_with_version = accession
          if record.id.startswith(accession + "."):
              try:
                  acc_with_version = "%s.%i" \
                                     % (accession,
                                        int(record.id.split(".", 1)[1]))
              except ValueError:
                  pass
          gi = self._get_annotation_str(record, "gi", just_first=True)
  
          descr = record.description
          if descr == "<unknown description>":
              descr = "."
          self._write_multi_line("DEFINITION", descr)
  
          self._write_single_line("ACCESSION", accession)
          if gi != ".":
              self._write_single_line("VERSION", "%s  GI:%s"
                                      % (acc_with_version, gi))
          else:
              self._write_single_line("VERSION", "%s" % (acc_with_version))
  
          # The NCBI only expect two types of link so far,
          # e.g. "Project:28471" and "Trace Assembly Archive:123456"
          # TODO - Filter the dbxrefs list to just these?
          self._write_multi_entries("DBLINK", record.dbxrefs)
  
          try:
              # List of strings
              # Keywords should be given separated with semi colons,
              keywords = "; ".join(record.annotations["keywords"])
              # with a trailing period:
              if not keywords.endswith("."):
                  keywords += "."
          except KeyError:
              # If no keywords, there should be just a period:
              keywords = "."
          self._write_multi_line("KEYWORDS", keywords)
  
          if "segment" in record.annotations:
              # Deal with SEGMENT line found only in segmented records,
              # e.g. AH000819
              segment = record.annotations["segment"]
              if isinstance(segment, list):
                  assert len(segment) == 1, segment
                  segment = segment[0]
              self._write_single_line("SEGMENT", segment)
  
          self._write_multi_line("SOURCE",
                                 self._get_annotation_str(record, "source"))
          # The ORGANISM line MUST be a single line, as any continuation is the taxonomy
          org = self._get_annotation_str(record, "organism")
          if len(org) > self.MAX_WIDTH - self.HEADER_WIDTH:
              org = org[:self.MAX_WIDTH - self.HEADER_WIDTH - 4] + "..."
          self._write_single_line("  ORGANISM", org)
          try:
              # List of strings
              # Taxonomy should be given separated with semi colons,
              taxonomy = "; ".join(record.annotations["taxonomy"])
              # with a trailing period:
              if not taxonomy.endswith("."):
                  taxonomy += "."
          except KeyError:
              taxonomy = "."
          self._write_multi_line("", taxonomy)
  
          if "references" in record.annotations:
              self._write_references(record)
  
          if "comment" in record.annotations:
              self._write_comment(record)
  
          handle.write("FEATURES             Location/Qualifiers\n")
          rec_length = len(record)
          for feature in record.features:
              self._write_feature(feature, rec_length)
          self._write_sequence(record)
          handle.write("//\n")
  
  
  class EmblWriter(_InsdcWriter):
      HEADER_WIDTH = 5
      QUALIFIER_INDENT = 21
      QUALIFIER_INDENT_STR = "FT" + " " * (QUALIFIER_INDENT - 2)
      QUALIFIER_INDENT_TMP = "FT   %s                "  # 21 if %s is empty
      FEATURE_HEADER = "FH   Key             Location/Qualifiers\n"
  
      def _write_contig(self, record):
          max_len = self.MAX_WIDTH - self.HEADER_WIDTH
          lines = self._split_contig(record, max_len)
          for text in lines:
              self._write_single_line("CO", text)
  
      def _write_sequence(self, record):
          LETTERS_PER_BLOCK = 10
          BLOCKS_PER_LINE = 6
          LETTERS_PER_LINE = LETTERS_PER_BLOCK * BLOCKS_PER_LINE
          POSITION_PADDING = 10
          handle = self.handle  # save looking up this multiple times
  
          if isinstance(record.seq, UnknownSeq):
              # We have already recorded the length, and there is no need
              # to record a long sequence of NNNNNNN...NNN or whatever.
              if "contig" in record.annotations:
                  self._write_contig(record)
              else:
                  # TODO - Can the sequence just be left out as in GenBank files?
                  handle.write("SQ   \n")
              return
  
          # Catches sequence being None
          data = self._get_seq_string(record).lower()
          seq_len = len(data)
  
          # Get the base alphabet (underneath any Gapped or StopCodon encoding)
          a = Alphabet._get_base_alphabet(record.seq.alphabet)
          if isinstance(a, Alphabet.DNAAlphabet):
              # TODO - What if we have RNA?
              a_count = data.count('A') + data.count('a')
              c_count = data.count('C') + data.count('c')
              g_count = data.count('G') + data.count('g')
              t_count = data.count('T') + data.count('t')
              other = seq_len - (a_count + c_count + g_count + t_count)
              handle.write("SQ   Sequence %i BP; %i A; %i C; %i G; %i T; %i other;\n"
                           % (seq_len, a_count, c_count, g_count, t_count, other))
          else:
              handle.write("SQ   \n")
  
          for line_number in range(0, seq_len // LETTERS_PER_LINE):
              handle.write("    ")  # Just four, not five
              for block in range(BLOCKS_PER_LINE):
                  index = LETTERS_PER_LINE * line_number + \
                      LETTERS_PER_BLOCK * block
                  handle.write((" %s" % data[index:index + LETTERS_PER_BLOCK]))
              handle.write(str((line_number + 1)
                               * LETTERS_PER_LINE).rjust(POSITION_PADDING))
              handle.write("\n")
          if seq_len % LETTERS_PER_LINE:
              # Final (partial) line
              line_number = (seq_len // LETTERS_PER_LINE)
              handle.write("    ")  # Just four, not five
              for block in range(BLOCKS_PER_LINE):
                  index = LETTERS_PER_LINE * line_number + \
                      LETTERS_PER_BLOCK * block
                  handle.write(
                      (" %s" % data[index:index + LETTERS_PER_BLOCK]).ljust(11))
              handle.write(str(seq_len).rjust(POSITION_PADDING))
              handle.write("\n")
  
      def _write_single_line(self, tag, text):
          assert len(tag) == 2
          line = tag + "   " + text
          if len(text) > self.MAX_WIDTH:
              warnings.warn("Line %r too long" % line, BiopythonWarning)
          self.handle.write(line + "\n")
  
      def _write_multi_line(self, tag, text):
          max_len = self.MAX_WIDTH - self.HEADER_WIDTH
          lines = self._split_multi_line(text, max_len)
          for line in lines:
              self._write_single_line(tag, line)
  
      def _write_the_first_lines(self, record):
          """Write the ID and AC lines."""
          if "." in record.id and record.id.rsplit(".", 1)[1].isdigit():
              version = "SV " + record.id.rsplit(".", 1)[1]
              accession = self._get_annotation_str(record, "accession",
                                                   record.id.rsplit(".", 1)[0],
                                                   just_first=True)
          else:
              version = ""
              accession = self._get_annotation_str(record, "accession",
                                                   record.id,
                                                   just_first=True)
  
          if ";" in accession:
              raise ValueError("Cannot have semi-colon in EMBL accession, %s"
                               % repr(str(accession)))
          if " " in accession:
              # This is out of practicallity... might it be allowed?
              raise ValueError("Cannot have spaces in EMBL accession, %s"
                               % repr(str(accession)))
  
          # Get the molecule type
          # TODO - record this explicitly in the parser?
          # Get the base alphabet (underneath any Gapped or StopCodon encoding)
          a = Alphabet._get_base_alphabet(record.seq.alphabet)
          if not isinstance(a, Alphabet.Alphabet):
              raise TypeError("Invalid alphabet")
          elif isinstance(a, Alphabet.DNAAlphabet):
              mol_type = "DNA"
              units = "BP"
          elif isinstance(a, Alphabet.RNAAlphabet):
              mol_type = "RNA"
              units = "BP"
          elif isinstance(a, Alphabet.ProteinAlphabet):
              mol_type = "PROTEIN"
              units = "AA"
          else:
              # Must be something like NucleotideAlphabet
              raise ValueError("Need a DNA, RNA or Protein alphabet")
  
          # Get the taxonomy division
          division = self._get_data_division(record)
  
          # TODO - Full ID line
          handle = self.handle
          # ID   <1>; SV <2>; <3>; <4>; <5>; <6>; <7> BP.
          # 1. Primary accession number
          # 2. Sequence version number
          # 3. Topology: 'circular' or 'linear'
          # 4. Molecule type
          # 5. Data class
          # 6. Taxonomic division
          # 7. Sequence length
          self._write_single_line("ID", "%s; %s; ; %s; ; %s; %i %s."
                                  % (accession, version, mol_type,
                                     division, len(record), units))
          handle.write("XX\n")
          self._write_single_line("AC", accession + ";")
          handle.write("XX\n")
  
      def _get_data_division(self, record):
          try:
              division = record.annotations["data_file_division"]
          except KeyError:
              division = "UNC"
          if division in ["PHG", "ENV", "FUN", "HUM", "INV", "MAM", "VRT",
                          "MUS", "PLN", "PRO", "ROD", "SYN", "TGN", "UNC",
                          "VRL", "XXX"]:
              # Good, already EMBL style
              #    Division                 Code
              #    -----------------        ----
              #    Bacteriophage            PHG
              #    Environmental Sample     ENV
              #    Fungal                   FUN
              #    Human                    HUM
              #    Invertebrate             INV
              #    Other Mammal             MAM
              #    Other Vertebrate         VRT
              #    Mus musculus             MUS
              #    Plant                    PLN
              #    Prokaryote               PRO
              #    Other Rodent             ROD
              #    Synthetic                SYN
              #    Transgenic               TGN
              #    Unclassified             UNC (i.e. unknown)
              #    Viral                    VRL
              #
              # (plus XXX used for submiting data to EMBL)
              pass
          else:
              # See if this is in GenBank style & can be converted.
              # Generally a problem as the GenBank groups are wider
              # than those of EMBL. Note that GenBank use "BCT" for
              # both bacteria and acherea thus this maps to EMBL's
              # "PRO" nicely.
              gbk_to_embl = {"BCT": "PRO",
                             "UNK": "UNC",
                             }
              try:
                  division = gbk_to_embl[division]
              except KeyError:
                  division = "UNC"
          assert len(division) == 3
          return division
  
      def _write_keywords(self, record):
          # Put the keywords right after DE line.
          # Each 'keyword' can have multiple words and spaces, but we
          # must not split any 'keyword' between lines.
          # TODO - Combine short keywords onto one line
          for keyword in record.annotations["keywords"]:
              self._write_single_line("KW", keyword)
          self.handle.write("XX\n")
  
      def _write_references(self, record):
          # The order should be RN, RC, RP, RX, RG, RA, RT, RL
          number = 0
          for ref in record.annotations["references"]:
              if not isinstance(ref, SeqFeature.Reference):
                  continue
              number += 1
              self._write_single_line("RN", "[%i]" % number)
              # TODO - support for RC line (needed in parser too)
              # TODO - support more complex record reference locations?
              if ref.location and len(ref.location) == 1:
                  self._write_single_line(
                      "RP", "%i-%i" % (ref.location[0].nofuzzy_start + 1,
                                       ref.location[0].nofuzzy_end))
              # TODO - record any DOI or AGRICOLA identifier in the reference object?
              if ref.pubmed_id:
                  self._write_single_line("RX", "PUBMED; %s." % ref.pubmed_id)
              if ref.consrtm:
                  self._write_single_line("RG", "%s" % ref.consrtm)
              if ref.authors:
                  # We store the AUTHORS data as a single string
                  self._write_multi_line("RA", ref.authors + ";")
              if ref.title:
                  # We store the title as a single string
                  self._write_multi_line("RT", '"%s";' % ref.title)
              if ref.journal:
                  # We store this as a single string - holds the journal name,
                  # volume, year, and page numbers of the citation
                  self._write_multi_line("RL", ref.journal)
              self.handle.write("XX\n")
  
      def _write_comment(self, record):
          # This is a bit complicated due to the range of possible
          # ways people might have done their annotation...
          # Currently the parser uses a single string with newlines.
          # A list of lines is also reasonable.
          # A single (long) string is perhaps the most natural of all.
          # This means we may need to deal with line wrapping.
          comment = record.annotations["comment"]
          if isinstance(comment, basestring):
              lines = comment.split("\n")
          elif isinstance(comment, (list, tuple)):
              lines = comment
          else:
              raise ValueError("Could not understand comment annotation")
          # TODO - Merge this with the GenBank comment code?
          if not lines:
              return
          for line in lines:
              self._write_multi_line("CC", line)
          self.handle.write("XX\n")
  
      def write_record(self, record):
          """Write a single record to the output file."""
  
          handle = self.handle
          self._write_the_first_lines(record)
  
          # PR line (0 or 1 lines only), project identifier
          #
          # Assuming can't use 2 lines, we should prefer newer GenBank
          # DBLINK BioProject:... entries over the older GenBank DBLINK
          # Project:... lines.
          #
          # In either case, seems EMBL usess just "PR    Project:..."
          # regardless of the type of ID (old numeric only, or new
          # with alpha prefix), e.g. for CP002497 NCBI now uses:
          #
          # DBLINK      BioProject: PRJNA60715
          #             BioSample: SAMN03081426
          #
          # While EMBL uses:
          #
          # XX
          # PR   Project:PRJNA60715;
          # XX
          #
          # Sorting ensures (new) BioProject:... is before old Project:...
          for xref in sorted(record.dbxrefs):
              if xref.startswith("BioProject:"):
                  self._write_single_line("PR", xref[3:] + ";")
                  handle.write("XX\n")
                  break
              if xref.startswith("Project:"):
                  self._write_single_line("PR", xref + ";")
                  handle.write("XX\n")
                  break
  
          # TODO - DT lines (date)
  
          descr = record.description
          if descr == "<unknown description>":
              descr = "."
          self._write_multi_line("DE", descr)
          handle.write("XX\n")
  
          if "keywords" in record.annotations:
              self._write_keywords(record)
  
          # Should this be "source" or "organism"?
          self._write_multi_line(
              "OS", self._get_annotation_str(record, "organism"))
          try:
              # List of strings
              taxonomy = "; ".join(record.annotations["taxonomy"]) + "."
          except KeyError:
              taxonomy = "."
          self._write_multi_line("OC", taxonomy)
          handle.write("XX\n")
  
          if "references" in record.annotations:
              self._write_references(record)
  
          if "comment" in record.annotations:
              self._write_comment(record)
  
          handle.write(self.FEATURE_HEADER)
          rec_length = len(record)
          for feature in record.features:
              self._write_feature(feature, rec_length)
          handle.write("XX\n")
  
          self._write_sequence(record)
          handle.write("//\n")
  
  
  class ImgtWriter(EmblWriter):
      HEADER_WIDTH = 5
      QUALIFIER_INDENT = 25  # Not 21 as in EMBL
      QUALIFIER_INDENT_STR = "FT" + " " * (QUALIFIER_INDENT - 2)
      QUALIFIER_INDENT_TMP = "FT   %s                    "  # 25 if %s is empty
      FEATURE_HEADER = "FH   Key                 Location/Qualifiers\n"
  
  if __name__ == "__main__":
      from Bio._utils import run_doctest
      run_doctest(verbose=0)
  