view NEWS @ 864:cfcbd13f6761
Added fileio.BioPythonFile as a method to parse unknown file formats [closes #106]
Biopython can parse more formats than EMBOSS, but surprisingly, it cannot do msf.
Also, there is no way to see in the current tests, where a test used biopython
or emboss for a particular IO task. This will likely be fixed with the 1.5.0 release
with the new fileio system. For now, Biopython has precedence over EMBOSS, so
an IO test of msf tests EMBOSS, and IO test of Stockholm tests Biopython.
| author |
Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
| date |
Mon, 25 Jul 2011 14:40:41 +0400 |
| parents |
da46b25fd67d |
| children |
b8f1c216bca8 |
line source
3 This is a code cleanup release.
4 Nothing should change in the interface or behaviour at all.
8 * new: Alignments, Sequences and Blocks now can have Markups, see the wiki
9 * new: File format 'markup' for storing alignment with arbitrary markups
10 * new: processor allpy.processors.Needle()
11 * new: method allpy.base.Alignment.rows_as_strings()
12 * new: method allpy.base.Alignment.row_as_list(sequence)
13 * new: method allpy.base.Alignment.row_as_string(sequence)
14 * new: columns_as_lists() returns list of lists, each has 'column' attribute
15 * new: javascript viewer colors columns by conservedness
19 * new: started NEWS file
20 * new: started tracking version numbers
