1.1 --- a/allpy/base.py	Thu Dec 16 22:30:32 2010 +0300
     1.2 +++ b/allpy/base.py	Thu Dec 16 23:42:14 2010 +0300
     1.3 @@ -179,10 +179,9 @@
     1.4  
     1.5          File must contain exactly one sequence.
     1.6          """
     1.7 -        sequences = fasta.parse_file(file)
     1.8 -        assert len(sequences) == 1
     1.9 -        name, description = sequences.keys()[0]
    1.10 -        return cls(sequences[header], name, description, file.name)
    1.11 +        sequence, = fasta.parse_file(file)
    1.12 +        name, description, body = sequence
    1.13 +        return cls(body, name, description, file.name)
    1.14  
    1.15  class Alignment(object):
    1.16      """Alignment. It is a list of Columns."""
    1.17 @@ -214,7 +213,7 @@
    1.18      def append_gapped_line(self, line, name='', description='', source='',
    1.19              gaps=default_gaps):
    1.20          """Add row from a line of one-letter codes and gaps."""
    1.21 -        Sequence = cls.sequence_type
    1.22 +        Sequence = self.sequence_type
    1.23          not_gap = lambda (i, char): char not in gaps
    1.24          without_gaps = util.remove_each(line, gaps)
    1.25          sequence = Sequence(without_gaps, name, description, source)
    1.26 @@ -226,7 +225,7 @@
    1.27          # - it's position in alignment (the first attached number, j)
    1.28          # - it's position in sequence (the second attached number, i)
    1.29          for i, (j, char) in enumerate(filter(not_gap, enumerate(line))):
    1.30 -            self.column_at(j)[seq] = sequence[i]
    1.31 +            self.column_at(j)[sequence] = sequence[i]
    1.32          self.sequences.append(sequence)
    1.33  
    1.34      def column_at(self, n):
    1.35 @@ -245,7 +244,7 @@
    1.36      def from_fasta(cls, file, gaps=default_gaps):
    1.37          """Create new alignment from FASTA file."""
    1.38          self = cls()
    1.39 -        for ((name, description), body) in fasta.parse_file(file):
    1.40 +        for (name, description, body) in fasta.parse_file(file):
    1.41              self.append_gapped_line(body, name, description, gaps)
    1.42          return self
    1.43  

     2.1 --- a/allpy/fasta.py	Thu Dec 16 22:30:32 2010 +0300
     2.2 +++ b/allpy/fasta.py	Thu Dec 16 23:42:14 2010 +0300
     2.3 @@ -1,9 +1,9 @@
     2.4 -def parse_fasta(file):
     2.5 +def parse_file(file):
     2.6      """Parse fasta file, remove spaces and newlines from sequence bodies.
     2.7  
     2.8 -    Return a dict of { (name, description) : sequence_body }.
     2.9 +    Return a list of tuples (name, description, sequence_body).
    2.10      """
    2.11 -    sequences = {}
    2.12 +    sequences = []
    2.13      for part in file.read().split(">"):
    2.14          header, _, body = part.partition("\n")
    2.15          header = header.lstrip(">").strip()
    2.16 @@ -11,10 +11,10 @@
    2.17          name = name.strip()
    2.18          description = description.strip()
    2.19          body = body.replace(" ", "").replace("\n", "")
    2.20 -        sequences[name, description] = body
    2.21 +        sequences.append((name, description, body))
    2.22      return sequences
    2.23  
    2.24 -def save_fasta(out_file, string, name, description='', long_line=70):
    2.25 +def save_file(out_file, string, name, description='', long_line=70):
    2.26      """ Saves given string to out_file in fasta_format
    2.27  
    2.28      Splits long lines to substrings of length=long_line