1.1 --- a/allpy/base.py	Thu Dec 16 19:17:08 2010 +0300
     1.2 +++ b/allpy/base.py	Thu Dec 16 19:24:22 2010 +0300
     1.3 @@ -10,6 +10,9 @@
     1.4  from Bio.PDB.DSSP import make_dssp_dict
     1.5  import data.codes
     1.6  
     1.7 +default_gaps = set((".", "-", "~"))
     1.8 +"""Set of characters to recoginze as gaps when parsing alignment."""
     1.9 +
    1.10  class MonomerType(object):
    1.11      """Class of monomer types.
    1.12  
    1.13 @@ -211,12 +214,13 @@
    1.14          for i, monomer in enumerate(sequence):
    1.15              self.column_at(i)[sequence] = monomer
    1.16  
    1.17 -    def append_gapped_line(self, line, name='', description='', source=''):
    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 -        not_gap = lambda (i, char): char != "-"
    1.23 -        no_gaps = line.replace("-", "")
    1.24 -        sequence = Sequence(no_gaps, name, description, source)
    1.25 +        not_gap = lambda (i, char): char not in gaps
    1.26 +        without_gaps = util.remove_each(line, gaps)
    1.27 +        sequence = Sequence(without_gaps, name, description, source)
    1.28          # The following line has some simple magic:
    1.29          # 1. attach natural numbers to monomers
    1.30          # 2. delete gaps
    1.31 @@ -241,11 +245,11 @@
    1.32      # ====================
    1.33  
    1.34      @classmethod
    1.35 -    def from_fasta(cls, file):
    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 -            self.append_gapped_line(body, name, description)
    1.41 +            self.append_gapped_line(body, name, description, gaps)
    1.42          return self
    1.43  
    1.44      def to_fasta(self, file):