allpy
changeset 444:36095a51e4c0
Tested and fixed Block.process(*, False, False)
In this ivokation process only copies gap patterns, not sequence names. It is
equivalent to calling Block._replace_column_contents.
Previously this function assumed self is Alignment and that each monomer in
self.sequences is visible in columns. This is false for Blocks.
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Tue, 15 Feb 2011 22:45:34 +0300 |
| parents | 63ea2a072f8d |
| children | d8c507743f12 |
| files | allpy/base.py |
| diffstat | 1 files changed, 12 insertions(+), 9 deletions(-) [+] |
line diff
1.1 --- a/allpy/base.py Tue Feb 15 22:32:14 2011 +0300 1.2 +++ b/allpy/base.py Tue Feb 15 22:45:34 2011 +0300 1.3 @@ -322,10 +322,10 @@ 1.4 if column == {}: 1.5 self.columns[n:n+1] = [] 1.6 1.7 - def _wipe(self): 1.8 - """Make all positions gaps (but keep sequences intact).""" 1.9 + def _wipe_row(self, sequence): 1.10 + """Turn all row positions into gaps (but keep sequences intact).""" 1.11 for column in self.columns: 1.12 - for sequence in list(column): 1.13 + if sequence in column: 1.14 del column[sequence] 1.15 1.16 def _merge(self, dst, new, merge): 1.17 @@ -353,19 +353,22 @@ 1.18 def _replace_column_contents(self, new): 1.19 """Replace column contents with those of `new` alignment. 1.20 1.21 - Synonym: copy gap patterns from `new` to `self`. 1.22 + In other words: copy gap patterns from `new` to `self`. 1.23 1.24 `self.sequences` and `new.sequences` should have the same contents. 1.25 """ 1.26 - self._wipe() 1.27 - not_gap = lambda (a,b): a != None 1.28 - for sequence, new_row in zip(self.sequences, new.rows_as_lists()): 1.29 - assert len(sequence) == len(filter(None, new_row.sequence)) 1.30 + for row, new_row in zip(self.rows_as_lists(), new.rows_as_lists()): 1.31 + sequence = row.sequence 1.32 + monomers = filter(None, row) 1.33 + print monomers 1.34 + print filter(None, new_row) 1.35 + assert len(monomers) == len(filter(None, new_row)) 1.36 + self._wipe_row(sequence) 1.37 non_gap_columns = [column 1.38 for column, monomer in zip(self.columns, new_row) 1.39 if monomer 1.40 ] 1.41 - for monomer, column in zip(sequence, non_gap_columns): 1.42 + for monomer, column in zip(monomers, non_gap_columns): 1.43 column[sequence] = monomer 1.44 1.45 def _replace_contents(self, new, copy_descriptions, copy_contents):