| age |
author |
description |
| Wed, 14 Dec 2011 19:45:57 +0300 |
Daniil Alexeyevsky |
Recorded changes in debian/changelog (not all of them, regretfully) |
| Wed, 14 Dec 2011 19:44:07 +0300 |
Daniil Alexeyevsky |
blocks3d-wt Debian: moved creation of /var/run/wt to initscript (as required by new Debian policy) |
| Mon, 28 Nov 2011 18:33:25 +0300 |
Daniil Alexeyevsky |
Fixed bug in processors: used Block class for reading alignment file. |
| Mon, 28 Nov 2011 17:27:45 +0300 |
Daniil Alexeyevsky |
Bugfix: _append_columns was in Column instead of Block by mistake |
| Tue, 22 Nov 2011 00:13:40 +0300 |
Daniil Alexeyevsky |
Fixed two bugs in one place: base Alignment/Block |
| Mon, 21 Nov 2011 19:16:25 +0300 |
Daniil Alexeyevsky |
Fixed regression in base.SequenceMarkup: remove was not working due to a naming error |
| Mon, 21 Nov 2011 18:40:16 +0300 |
Daniil Alexeyevsky |
Added class Column to different dna/rna/protein modules too |
| Mon, 21 Nov 2011 18:39:34 +0300 |
Daniil Alexeyevsky |
Added dna.Sequence.reverse_complemented() |
| Mon, 21 Nov 2011 18:05:14 +0300 |
Daniil Alexeyevsky |
processors.Needle does not yet allow : in sequence names |
| Wed, 09 Nov 2011 00:49:31 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 09 Nov 2011 00:49:25 +0300 |
Daniil Alexeyevsky |
Added internal support for new file format: FastQ |
| Tue, 08 Nov 2011 19:12:37 +0300 |
Daniil Alexeyevsky |
allpy.processor.ExternalCommand: close file descriptors from temporary files |
| Mon, 07 Nov 2011 18:20:12 +0300 |
Boris Nagaev |
sbbs_2009: fix a typo in comments |
| Fri, 04 Nov 2011 13:38:28 +0300 |
Daniil Alexeyevsky |
allpy.fileio: a little code cleanup |
| Fri, 04 Nov 2011 11:02:26 +0300 |
Daniil Alexeyevsky |
Moved allpy.fileio.bio.BioPythonFile.supports (which was static method) -> allpy.fileio.bio.supports (which is logical) |
| Fri, 04 Nov 2011 00:42:37 +0300 |
Daniil Alexeyevsky |
Split allpy.fileio into many files |
| Thu, 03 Nov 2011 23:34:03 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Thu, 03 Nov 2011 23:33:58 +0300 |
Daniil Alexeyevsky |
Added util markup_to_file.py that converts sequence markup from markup file to fake sequences in output format |
| Thu, 03 Nov 2011 15:51:04 +0300 |
Boris Nagaev |
test: add ex2.fasta |
| Thu, 03 Nov 2011 15:47:23 +0300 |
Boris Nagaev |
test: rename aln1.fasta to ex1.fasta |
| Thu, 03 Nov 2011 15:40:25 +0300 |
Boris Nagaev |
remove some debugging prints from allpy library |
| Thu, 03 Nov 2011 14:27:53 +0300 |
Boris Nagaev |
pair_cores/compare_aln_3d: remove -o option |
| Wed, 02 Nov 2011 19:44:22 +0300 |
Daniil Alexeyevsky |
Debian changelog entry for previous commit |
| Wed, 02 Nov 2011 19:42:48 +0300 |
Daniil Alexeyevsky |
Fixed symlink in blocks3d debian package |
| Tue, 01 Nov 2011 18:45:31 +0300 |
Daniil Alexeyevsky |
Turned output of compare_aln_3d to a more regular format, simpler to describe |
| Fri, 28 Oct 2011 20:40:55 +0300 |
Boris Nagaev |
remove junk code from structure.get_id_parse() |
| Fri, 28 Oct 2011 00:42:17 +0300 |
Boris Nagaev |
add program compare_aln_3d.py |
| Thu, 27 Oct 2011 12:26:19 +0300 |
Boris Nagaev |
pair-cores/score-all: sort output lines |
| Wed, 26 Oct 2011 22:44:07 +0300 |
Boris Nagaev |
add script pair_cores/against-database.py |
| Wed, 26 Oct 2011 22:22:49 +0300 |
Boris Nagaev |
extract_prefab: fix a bug causing only one sequence from alignment markuped |
| Wed, 26 Oct 2011 00:02:43 +0300 |
Boris Nagaev |
add script to generate score table (pair-cores against some database) |
| Tue, 25 Oct 2011 22:28:14 +0300 |
Boris Nagaev |
remove old programs pair_cores/score.py and pair_cores/score_all.py |
| Tue, 25 Oct 2011 21:47:56 +0300 |
Boris Nagaev |
add program extract_prefab.py |
| Tue, 25 Oct 2011 21:24:02 +0300 |
Boris Nagaev |
add *args binding to utility class Binder |
| Fri, 21 Oct 2011 17:55:19 +0300 |
Boris Nagaev |
move helper class Binder from pair_cores_all.py to allpy/util.py |
| Fri, 21 Oct 2011 13:48:47 +0300 |
Boris Nagaev |
add pymol superimposition feature (draft) |
| Thu, 13 Oct 2011 16:28:26 +0400 |
Daniil Alexeyevsky |
Rebuilt blocks3d-wt with newer wt |
| Tue, 11 Oct 2011 17:21:44 +0400 |
Daniil Alexeyevsky |
MarkupIOMixin: added attribute quotes to allow quotation around markup serialized string; fixed implementation of SequenceCaseMarkup based on that; [closes #125] |
| Mon, 10 Oct 2011 22:14:47 +0400 |
Boris Nagaev |
add test alignment to .hgignore |
| Mon, 10 Oct 2011 22:03:58 +0400 |
Boris Nagaev |
fix pair_cores: add default value for argument ignore_one_ss of homology_from_3d() |
| Wed, 05 Oct 2011 20:42:15 +0300 |
Boris Nagaev |
structure: allow to load custom pdbs |
| Fri, 23 Sep 2011 14:10:25 +0400 |
Boris Nagaev |
fix error caused by applying secondary structure markup |
| Fri, 23 Sep 2011 14:06:43 +0400 |
Boris Nagaev |
pair_cores.py: pass forgotten ignore_one_ss argument to pair_core_parts() |
| Fri, 23 Sep 2011 14:00:34 +0400 |
Boris Nagaev |
test: add make rule alignments, downloading simple alignment |
| Fri, 23 Sep 2011 13:41:42 +0400 |
Boris Nagaev |
blocks3d/www: fix false negatives in conservative columns |
| Mon, 19 Sep 2011 20:52:53 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Mon, 19 Sep 2011 20:06:03 +0400 |
Daniil Alexeyevsky |
Added .hgeol rules for EVERY file in the repository (so it seems). closes #118 |
| Mon, 19 Sep 2011 19:43:42 +0400 |
Daniil Alexeyevsky |
Changed EOLs in .hgignore to UNIX style, see #118 |
| Sun, 18 Sep 2011 16:32:59 +0400 |
Boris Nagaev |
Geometrical core improvement: ignore cores, owned by one SS element |
| Sun, 18 Sep 2011 15:11:49 +0400 |
Boris Nagaev |
add test for secondary structure markup for sequence |
| Sun, 18 Sep 2011 15:08:40 +0400 |
Boris Nagaev |
add secondary structure markup for sequence |
| Sun, 18 Sep 2011 12:46:35 +0400 |
Boris Nagaev |
blocks3d/www: yui-compressor turned into optional dependency |
| Sun, 18 Sep 2011 12:38:10 +0400 |
Boris Nagaev |
DownloadPdb, CachedDownloadPdb: change case of pdb code to lower |
| Sun, 18 Sep 2011 12:32:38 +0400 |
Boris Nagaev |
CachedDownloadPdb: fix a bug causing most of downloaded pdb files not to save |
| Sun, 18 Sep 2011 12:23:57 +0400 |
Boris Nagaev |
blocks3d.py: add option -S not to save downloaded pdb to cache_dir |
| Sun, 18 Sep 2011 12:23:09 +0400 |
Boris Nagaev |
CachedDownloadPdb: add an argument not to save downloaded pdb to cache_dir |
| Sun, 18 Sep 2011 11:57:45 +0400 |
Boris Nagaev |
blobks3d.py: default don't use full Bron-Kerbosh at all on the first stage, only use fast algorithm |
| Thu, 15 Sep 2011 23:01:51 +0400 |
Boris Nagaev |
blocks3d/www: add downloaded utf8_encode.js to .hgignore |
| Thu, 15 Sep 2011 17:50:13 +0400 |
Boris Nagaev |
blocks3d: cache downloaded PDB's by default |
| Thu, 15 Sep 2011 17:44:53 +0400 |
Boris Nagaev |
fix blocks3d/www: add changes forgotten while migrating to Makefile |
