1.1 --- a/allpy/base.py	Thu Jul 07 12:53:53 2011 +0400
     1.2 +++ b/allpy/base.py	Thu Jul 07 19:21:12 2011 +0400
     1.3 @@ -221,17 +221,12 @@
     1.4          If sequences in file have gaps (detected as characters belonging to
     1.5          `gaps` set), treat them accordingly.
     1.6          """
     1.7 -        sequences = []
     1.8 -        io = fileio.File(file, format)
     1.9 -        for name, description, body in io.read_strings():
    1.10 -            self.append_row_from_string(body, name, description, file.name, gaps)
    1.11 +        fileio.File(file, format, gaps=gaps).read_alignment(self)
    1.12          return self
    1.13  
    1.14      def to_file(self, file, format='fasta', gap='-'):
    1.15          """Write alignment in FASTA file as sequences with gaps."""
    1.16 -        strings = [(s, s.sequence.name, s.sequence.description)
    1.17 -            for s in self.rows_as_strings()]
    1.18 -        fileio.File(file, format).write_strings(strings)
    1.19 +        fileio.File(file, format, gaps=gap).write_alignment(self)
    1.20  
    1.21      # Data access methods for alignment
    1.22      # =================================

     2.1 --- a/allpy/fileio.py	Thu Jul 07 12:53:53 2011 +0400
     2.2 +++ b/allpy/fileio.py	Thu Jul 07 19:21:12 2011 +0400
     2.3 @@ -5,19 +5,37 @@
     2.4  
     2.5  class File(object):
     2.6      """Automatical file IO."""
     2.7 -    def __new__(cls, file, format="fasta"):
     2.8 +    def __new__(cls, file, format="fasta", **kw):
     2.9          if format == "fasta":
    2.10 -            return FastaFile(file)
    2.11 +            return FastaFile(file, **kw)
    2.12          else:
    2.13 -            return EmbossFile(file, format)
    2.14 +            return EmbossFile(file, format, **kw)
    2.15  
    2.16 -class FastaFile(object):
    2.17 +class AlignmentFile(object):
    2.18 +    """Some helpers."""
    2.19 +
    2.20 +    def __init__(self, file, format='fasta', gaps='-', wrap_column=70):
    2.21 +        self.file = file
    2.22 +        self.format = format
    2.23 +        self.gaps = gaps
    2.24 +        self.wrap_column = wrap_column
    2.25 +
    2.26 +    def write_alignment(self, alignment):
    2.27 +        """Append alignment to the file."""
    2.28 +        self.write_strings(
    2.29 +            (row, row.sequence.name, row.sequence.description)
    2.30 +            for row in alignment.rows_as_strings(self.gaps)
    2.31 +        )
    2.32 +
    2.33 +    def read_alignment(self, alignment):
    2.34 +        """Read alignment from the file."""
    2.35 +        append_row = alignment.append_row_from_string
    2.36 +        for name, description, body in self.read_strings():
    2.37 +            append_row(body, name, description, file.name, self.gaps)
    2.38 +
    2.39 +class FastaFile(AlignmentFile):
    2.40      """Fasta parser & writer."""
    2.41  
    2.42 -    def __init__(self, file, wrap_column=70):
    2.43 -        self.file = file
    2.44 -        self.wrap_column = wrap_column
    2.45 -
    2.46      def write_string(self, string, name, description=''):
    2.47          """Append one sequence to file."""
    2.48          if description:
    2.49 @@ -49,13 +67,9 @@
    2.50              body = util.remove_each(body, " \n\r\t\v")
    2.51              yield (name, description, body)
    2.52  
    2.53 -class EmbossFile(object):
    2.54 +class EmbossFile(AlignmentFile):
    2.55      """Parser & writer for file formats supported by EMBOSS."""
    2.56  
    2.57 -    def __init__(self, file, format):
    2.58 -        self.file = file
    2.59 -        self.format = format
    2.60 -
    2.61      def write_strings(self, sequences):
    2.62          """Write sequences to file."""
    2.63          pipe = Popen(['seqret', 'stdin', '%s::stdout' % self.format],