1.1 --- a/geometrical_core/geometrical_core.py	Sun Oct 24 16:58:06 2010 +0400
     1.2 +++ b/geometrical_core/geometrical_core.py	Sun Oct 24 17:06:15 2010 +0400
     1.3 @@ -121,3 +121,7 @@
     1.4      print 'Error: provide both pdb and spt file or none of them'
     1.5      exit()
     1.6  
     1.7 +
     1.8 +
     1.9 +
    1.10 +

     2.1 --- a/lib/block.py	Sun Oct 24 16:58:06 2010 +0400
     2.2 +++ b/lib/block.py	Sun Oct 24 17:06:15 2010 +0400
     2.3 @@ -40,7 +40,7 @@
     2.4          self.sequences = sequences
     2.5          self.positions = positions
     2.6  
     2.7 -    def save_fasta(self, out_file, long_line=60):
     2.8 +    def save_fasta(self, out_file, long_line=60, gap='-'):
     2.9          """
    2.10          Saves alignment to given file in fasta-format 
    2.11          Splits long lines to substrings of length=long_line
    2.12 @@ -112,21 +112,21 @@
    2.13                      break
    2.14          return GCs
    2.15      
    2.16 -    def xstring(self, x='X'):
    2.17 +    def xstring(self, x='X', gap='-'):
    2.18          """
    2.19 -        Returns string consisting of '-' and chars x at self.positions
    2.20 +        Returns string consisting of gap chars and chars x at self.positions
    2.21          Length of returning string = length of project
    2.22          """
    2.23          monomers = [False] * len(self.project)
    2.24          for i in self.positions:
    2.25              monomers[i] = True
    2.26 -        return ''.join([x if m else '-' for m in monomers])
    2.27 +        return ''.join([x if m else gap for m in monomers])
    2.28      
    2.29 -    def save_xstring(self, out_file, name, description='', x='X'):
    2.30 +    def save_xstring(self, out_file, name, description='', x='X', gap='-'):
    2.31          """
    2.32          Save xstring and name in fasta format
    2.33          """
    2.34          out_file.write(">%(name)s %(description)s \n" % \
    2.35          {'name':name, 'description':description})
    2.36          
    2.37 -        out_file.write(">%(xstring)s \n" % {'xstring':self.xstring()})
    2.38 +        out_file.write(">%(xstring)s \n" % {'xstring':self.xstring(x=x, gap=gap)})

     3.1 --- a/lib/project.py	Sun Oct 24 16:58:06 2010 +0400
     3.2 +++ b/lib/project.py	Sun Oct 24 17:06:15 2010 +0400
     3.3 @@ -153,13 +153,13 @@
     3.4              project.alignment[sequence] = sequence.monomers + [None] * gaps_count
     3.5          return project
     3.6      
     3.7 -    def save_fasta(self, out_file, long_line=60):
     3.8 +    def save_fasta(self, out_file, long_line=60, gap='-'):
     3.9          """
    3.10          Saves alignment to given file
    3.11          Splits long lines to substrings of length=long_line
    3.12          To prevent this, set long_line=None 
    3.13          """
    3.14 -        Block(self).save_fasta(out_file, long_line)
    3.15 +        Block(self).save_fasta(out_file, long_line=long_line, gap=gap)
    3.16          
    3.17      def muscle_align(self):
    3.18          """