view NEWS @ 1101:41a167bbf150
Fixed a serious bug with saving sequence markups when alignment does not have all of the sequence monomers
| author |
Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
| date |
Sat, 09 Jun 2012 21:03:13 +0400 |
| parents |
452ac0c16295 |
| children |
|
line source
3 This release collects a lot of changes that happened during half year. Most
6 * thorough testing of the core which discovered bugs in `
realign`
7 (fixes were back-ported into 1
.4
.0
too),
8 * greatly improved markups support and markups IO
9 (but it is still somewhat not user-friendly enough yet),
10 * utils `
markup_to_file`
and `
markup_to_html`
12 * and a lot of work on `
blocks3d`
and `
pair_cores`
with many new features,
13 fixes, added web-interface for `
pair_cores`
(clone of the `
blocks3d`
18 * change(!
): removed a lot of dead / obsolete code: `
allpy.markup`
(not to be
19 confused with `
allpy.markups`
), sandbox, `
pytale`
, `
sec_str`
20 * change: a lot of code cleanup
21 * change: replaced direct code inclusions from other projectd into allpy with
22 Makefiles to download the necessary code.
23 * new(!
): `
markup_to_file`
util for converting `
.markup`
to e.g `
.fasta`
24 (by adding pseudo sequences consisting of markup)
25 * new(!
): `
markup_to_html`
util for visually displaying markups in HTML
26 * bugfix: `
Muscle`
processor became incompatible with newer muscle
28 In allpy core (allpy.base, allpy.dna, allpy.protein, allpy.rna, fllpy.fileio):
30 * change: Allow markup to be tagged as saved / not saved (closes #83
)
31 * change(!
): fileio overhaul; split one giant module into several; many bugfixes
32 * new: `
fileio`
added internal support for `
FastQ`
(the new Illumina one)
33 * new: method `
dna.Sequence.reverse_complement()`
34 * bugfix(!
): until this release `
alignment.realign(...)`
could lose monomers
35 * bugfix: dna module has seen some use, minimal bugfixes followed
39 * new: added `
MarkupIOMixin`
which simplifies defining savable markup classes
40 * new: added pre-defined generic markups for simple data types (int, char,
45 * change: geometrical cores produces less false negatives by ignoring cores
46 contained within a single secondary-structure unit
47 * change: structure.ChachedDownloadPdb: option to discard downloaded files
48 * change: improved command-line interface of pair_cores (display defaults)
49 * change: blocks3d builds high blocks using MonomerHomology
50 * change: blocks3d() allows to specify pre-computed pair cores as `
parts`
51 * change: new method blocks_from_homology()
52 * new: draft feature for pymol superimposition
53 * new: allow to load custom pdbs (allpy.structure)
54 * new: web interface for pair-cores (similar to the existing for blocks3d)
58 This release was internal.
59 Please refer to changes in the 1
.4
.3
release, since 1
.4
.2
never made public.
63 This would have been a code cleanup release.
64 Please refer to changes in the 1
.4
.3
release, since 1
.4
.1
never made public.
68 * new: Alignments, Sequences and Blocks now can have Markups, see the wiki
69 * new: File format 'markup' for storing alignment with arbitrary markups
70 * new: processor `
allpy.processors.Needle()`
71 * new: method `
allpy.base.Alignment.rows_as_strings()`
72 * new: method `
allpy.base.Alignment.row_as_list(sequence)`
73 * new: method `
allpy.base.Alignment.row_as_string(sequence)`
74 * new: `
columns_as_lists()`
returns list of lists, each has `
column`
attribute
75 * new: javascript viewer colors columns by conservedness
79 * new: started NEWS file
80 * new: started tracking version numbers
