1.1 --- a/allpy/base.py	Tue Feb 01 00:20:24 2011 +0300
     1.2 +++ b/allpy/base.py	Tue Feb 01 17:11:33 2011 +0300
     1.3 @@ -49,9 +49,8 @@
     1.4          """Create all relevant subclasses of Monomer."""
     1.5          # NB. The table uses letters d, r, p for types,
     1.6          # while we use full words; hence, we compare by first letter
     1.7 -        for type, code1, is_modified, code3, name in codes:
     1.8 -            if type[0] == cls.type[0]:
     1.9 -                cls._subclass(name, code1, code3, is_modified)
    1.10 +        for code1, is_modified, code3, name in codes:
    1.11 +            cls._subclass(name, code1, code3, is_modified)
    1.12  
    1.13      @classmethod
    1.14      def from_code1(cls, code1):
    1.15 @@ -107,7 +106,7 @@
    1.16      @classmethod
    1.17      def from_monomers(cls, monomers=[], name=None, description=None, source=None):
    1.18          """Create sequence from a list of monomer objecst."""
    1.19 -        result = cls()
    1.20 +        result = cls(monomers)
    1.21          if name:
    1.22              result.name = name
    1.23          if description:
    1.24 @@ -194,7 +193,7 @@
    1.25          """
    1.26          assert format == 'fasta', "We don't support other formats yet"
    1.27          for (name, description, body) in fasta.parse_file(file):
    1.28 -            self.append_row(body, name, description, file.name, gaps)
    1.29 +            self.append_row_from_string(body, name, description, file.name, gaps)
    1.30          return self
    1.31  
    1.32      def to_file(self, file, format='fasta'):
    1.33 @@ -314,7 +313,7 @@
    1.34      def _wipe(self):
    1.35          """Make all positions gaps (but keep sequences intact)."""
    1.36          for column in self.columns:
    1.37 -            for sequence in column:
    1.38 +            for sequence in list(column.keys()):
    1.39                  del column[sequence]
    1.40  
    1.41      def _merge(self, dst, new, merge):
    1.42 @@ -358,7 +357,7 @@
    1.43          """Replace alignment contents with those of other alignment."""
    1.44          if copy_contents:
    1.45              self._replace_sequence_contents(new, copy_descriptions)
    1.46 -        self._replace_column_conents(new)
    1.47 +        self._replace_column_contents(new)
    1.48  
    1.49      def process(self, function, copy_descriptions=True, copy_contents=True):
    1.50          """Apply function to the alignment (or block); inject results back.

     2.1 --- a/allpy/processors.py	Tue Feb 01 00:20:24 2011 +0300
     2.2 +++ b/allpy/processors.py	Tue Feb 01 17:11:33 2011 +0300
     2.3 @@ -15,14 +15,13 @@
     2.4          self.command = command
     2.5  
     2.6      def __call__(self, block):
     2.7 -        infile = NamedTemporaryFile(delete=false)
     2.8 -        outfile = NamedTemporaryFile('r', delete=false)
     2.9 -        outfile.close()
    2.10 +        infile = NamedTemporaryFile(delete=False)
    2.11 +        outfile = NamedTemporaryFile('r', delete=False)
    2.12          block.to_file(infile)
    2.13          infile.close()
    2.14          os.system(self.command % {'infile': infile.name, 'outfile': outfile.name})
    2.15 -        Alignment = block.__base__
    2.16 -        new_alignment = Alignment().append_file(outfile))
    2.17 +        Alignment = block.__class__
    2.18 +        new_alignment = Alignment().append_file(outfile)
    2.19          os.unlink(infile.name)
    2.20          os.unlink(outfile.name)
    2.21          return new_alignment

     3.1 --- a/test/usecase1.py	Tue Feb 01 00:20:24 2011 +0300
     3.2 +++ b/test/usecase1.py	Tue Feb 01 17:11:33 2011 +0300
     3.3 @@ -1,4 +1,5 @@
     3.4  from allpy import protein
     3.5 +from allpy import processors
     3.6  
     3.7  # Create sequences from string representation of sequence body
     3.8  sequence_1 = protein.Sequence.from_string("mkstf", name="E2E4")
     3.9 @@ -8,7 +9,7 @@
    3.10  alignment = protein.Alignment()
    3.11  alignment.append_sequence(sequence_1)
    3.12  alignment.append_sequence(sequence_2)
    3.13 -alignment.realign("muscle")
    3.14 +alignment.process(processors.Muscle())
    3.15  
    3.16  # For each sequence, print number of gaps and non-gaps in alignment
    3.17  for row in alignment.rows():
    3.18 @@ -32,4 +33,4 @@
    3.19  print " ".join(map(str, gaps))
    3.20  
    3.21  # Write alignment to file
    3.22 -alignment.to_fasta(open("new_file.fasta", "w"))
    3.23 +alignment.to_file(open("new_file.fasta", "w"))