1.1 --- a/allpy/fileio.py	Fri Jul 15 17:13:01 2011 +0400
     1.2 +++ b/allpy/fileio.py	Fri Jul 15 18:01:31 2011 +0400
     1.3 @@ -102,7 +102,8 @@
     1.4      record type. Header is a sequence of lines, each in format `key: value`.
     1.5      Content, if present, is separated from header with an empty line.
     1.6  
     1.7 -    Type names and header key names are case-insensitive.
     1.8 +    Type names and header key names are case-insensitive and '-' and '_' in
     1.9 +    them are equivalent.
    1.10  
    1.11      Known record types now are:
    1.12  
    1.13 @@ -112,14 +113,14 @@
    1.14  
    1.15      Example::
    1.16  
    1.17 -        sequence_markup
    1.18 -        sequence_name: cyb5_mouse
    1.19 -        sequence_description:
    1.20 +        sequence-markup
    1.21 +        sequence-name: cyb5_mouse
    1.22 +        sequence-description:
    1.23          name: pdb_residue_number
    1.24          type: SequencePDBResidueNumberMarkup
    1.25          markup: -,12,121,122,123,124,13,14,15,-,-,16
    1.26  
    1.27 -        alignment_markup
    1.28 +        alignment-markup
    1.29          name: geometrical_core
    1.30          type: AlignmentGeometricalCoreMarkup
    1.31          markup: -,-,-,-,+,+,+,-,-,-,+,+,-,-,-,-
    1.32 @@ -161,9 +162,10 @@
    1.33      def write_record(self, record):
    1.34          """Write record to file. Add new line before every but first record."""
    1.35          self.write_empty_line()
    1.36 -        self.file.write('%s\n' % record['type'])
    1.37 +        self.file.write('%s\n' % self.normalize('write', record['type']))
    1.38          del record['type']
    1.39          for key, value in record.items():
    1.40 +            key = self.normalize('write', key)
    1.41              self.file.write('%s: %s\n' % (key, value))
    1.42  
    1.43      def write_empty_line(self):
    1.44 @@ -207,14 +209,14 @@
    1.45  
    1.46      def read_record(self, alignment, type):
    1.47          """Read record headers and record payload."""
    1.48 -        type = type.strip().lower()
    1.49 +        type = self.normalize('read', type)
    1.50          record = {'type': type}
    1.51          for line in self.file:
    1.52              if line.strip() == "":
    1.53                  self.read_payload(alignment, record, type)
    1.54                  return record
    1.55              key, value = line.split(':', 1)
    1.56 -            key = key.strip().lower()
    1.57 +            key = self.normalize('read', key)
    1.58              value = value.strip()
    1.59              record[key] = value
    1.60          return record
    1.61 @@ -225,6 +227,13 @@
    1.62              io = File(self.file, record.get('format', 'fasta'), gaps=self.gaps)
    1.63              io.read_alignment(alignment)
    1.64  
    1.65 +    @staticmethod
    1.66 +    def normalize(for_what, string):
    1.67 +        if for_what == 'read':
    1.68 +            return string.strip().replace('-', '_').lower()
    1.69 +        if for_what == 'write':
    1.70 +            return string.strip().replace('_', '-').capitalize()
    1.71 +
    1.72  class EmbossFile(AlignmentFile):
    1.73      """Parser & writer for file formats supported by EMBOSS."""
    1.74  

     2.1 --- a/allpy/markups.py	Fri Jul 15 17:13:01 2011 +0400
     2.2 +++ b/allpy/markups.py	Fri Jul 15 18:01:31 2011 +0400
     2.3 @@ -26,7 +26,7 @@
     2.4  
     2.5      @classmethod
     2.6      def from_record(cls, container, record, name=None):
     2.7 -        assert record['io-class'] == 'IntMarkup'
     2.8 +        assert record['io_class'] == 'IntMarkup'
     2.9          result = container.add_markup(name, markup_class=cls)
    2.10          separator = record.get('separator', ',')
    2.11          values = record['markup'].split(separator)
    2.12 @@ -42,7 +42,7 @@
    2.13                  return ""
    2.14              return str(value)
    2.15          values = [fmt(self.get(key)) for key in self.sorted_keys()]
    2.16 -        return {'markup': ','.join(values), 'io-class': 'IntMarkup'}
    2.17 +        return {'markup': ','.join(values), 'io_class': 'IntMarkup'}
    2.18  
    2.19  class SequenceNumberMarkup(base.SequenceMarkup):
    2.20  
    2.21 @@ -89,7 +89,7 @@
    2.22  
    2.23      @classmethod
    2.24      def from_record(cls, container, record, name=None):
    2.25 -        assert record['io-class'] == 'SequenceCaseMarkup'
    2.26 +        assert record['io_class'] == 'SequenceCaseMarkup'
    2.27          result = container.add_markup(name, markup_class=cls)
    2.28          markup = record['markup']
    2.29          assert markup[0] == markup[-1] == "'"
    2.30 @@ -111,7 +111,7 @@
    2.31                  markup += monomer.code1.upper()
    2.32              elif case == 'lower':
    2.33                  markup += monomer.code1.lower()
    2.34 -        return {'markup': "'%s'" % markup, 'io-class': 'SequenceCaseMarkup'}
    2.35 +        return {'markup': "'%s'" % markup, 'io_class': 'SequenceCaseMarkup'}
    2.36  
    2.37  class SequencePdbResiMarkup(base.SequenceMarkup, IntMarkupMixin):
    2.38      name = 'pdb_resi'