allpy

changeset 1080:fdc2d3594a3e
allpy.base: Added decency verification function to alignments (closes #98) Currently, the verification function asserts that no two sequences in an alignment have the same identifier.
author: Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date: Wed, 30 May 2012 12:43:09 +0400
parents: 9d4f28e3903a
children: 43b5207a70d7
files: allpy/base.py
diffstat: 1 files changed, 15 insertions(+), 0 deletions(-) [+]
[-]

allpy/base.py 15 allpy/base.py 15
allpy/base.py 15
     1.1 --- a/allpy/base.py	Wed May 30 12:33:22 2012 +0400
     1.2 +++ b/allpy/base.py	Wed May 30 12:43:09 2012 +0400
     1.3 @@ -494,9 +494,24 @@
     1.4  
     1.5          This is the same as process(function, False, False)
     1.6          """
     1.7 +        self.verify()
     1.8          new = function(self)
     1.9          self._replace_column_contents(new)
    1.10  
    1.11 +    # Helpers
    1.12 +    # =================================
    1.13 +
    1.14 +    def verify(self):
    1.15 +        """Make sure the alignment is decent. Raise an exception otherwise.
    1.16 +
    1.17 +        I.e.:
    1.18 +
    1.19 +        * it has no sequences with the same seq.name
    1.20 +        """
    1.21 +        seq_names = set(seq.names for seq in self.sequences)
    1.22 +        assert len(seq_names) == len(self.sequences), \
    1.23 +            "Alignment has sequences with the same identifier"
    1.24 +
    1.25  class Column(dict):
    1.26      """Column of alignment.
    1.27