| age |
author |
description |
| Sat, 25 Feb 2012 22:08:17 +0400 |
Boris Nagaev |
blocks3d: do not use pymol output feature of allpy trunc1.4.2 |
| Sat, 25 Feb 2012 22:06:38 +0400 |
Boris Nagaev |
pair-cores and geometrical-core: do not use ignore_one_ss feature of allpy trunc1.4.2 |
| Sat, 25 Feb 2012 21:56:17 +0400 |
Boris Nagaev |
blocks3d: do not use ignore_one_ss feature of allpy trunc1.4.2 |
| Sat, 25 Feb 2012 21:33:45 +0400 |
Boris Nagaev |
revert regression, introduced in 61bafa71cae7 for compatibility with allpy 1.4.0 |
| Sat, 25 Feb 2012 20:31:42 +0400 |
Daniil Alexeyevsky |
Added note to ss markup that it is going to be eliminated soon |
| Sat, 25 Feb 2012 20:30:13 +0400 |
Daniil Alexeyevsky |
Fix test for ss markup (which will anyway be eliminated soon); (see #138) |
| Sat, 25 Feb 2012 20:16:51 +0400 |
Daniil Alexeyevsky |
allpy.processors: use NamedTemporaryFile(..., delete=True) in favour of removing the files manually (closes #137) |
| Sat, 25 Feb 2012 19:25:42 +0400 |
Daniil Alexeyevsky |
Fixed reference to Column in allpy.base, which referred to closure instead of self.types (closes #138) |
| Sat, 25 Feb 2012 19:11:32 +0400 |
Daniil Alexeyevsky |
Automated merge |
| Sat, 25 Feb 2012 18:44:05 +0400 |
Daniil Alexeyevsky |
More sensible error message for _append_columns on an empty Block |
| Sat, 25 Feb 2012 18:54:15 +0400 |
Daniil Alexeyevsky |
New debian package build for python-allpy1.4.0 |
| Sat, 25 Feb 2012 18:50:58 +0400 |
Daniil Alexeyevsky |
Backported fixes to Alignment.realign(), Markup.remove(), processors.Muscle(), *.Column.types from default branch (revs [853],[931],[932],[933],[934],[952],[954])1.4.0 |
| Sat, 25 Feb 2012 17:42:45 +0400 |
Daniil Alexeyevsky |
Exported some unknown bnagaevs changes of blocks3d as a new debian package1.4.2 |
| Wed, 15 Feb 2012 19:54:06 +0400 |
Boris Nagaev |
make blocks3d compatible with allpy 1.4.01.4.2 |
| Wed, 15 Feb 2012 19:44:59 +0400 |
Boris Nagaev |
blocks-3d/wt: fix fasta example (unindent it)1.4.2 |
| Wed, 15 Feb 2012 19:25:30 +0400 |
Daniil Alexeyevsky |
pseudo-release 1.4.2 for the sake of updating blocks3d web-interface1.4.2 |
| Wed, 15 Feb 2012 19:54:06 +0400 |
Boris Nagaev |
make blocks3d compatible with allpy 1.4.0 |
| Wed, 15 Feb 2012 19:44:59 +0400 |
Boris Nagaev |
blocks-3d/wt: fix fasta example (unindent it) |
| Wed, 15 Feb 2012 16:37:23 +0400 |
Daniil Alexeyevsky |
Added SequenceCharMarkup to use with user-generated one-letter markups that can be saved to fasta later (see utils/markup_to_file.py) |
| Wed, 15 Feb 2012 16:21:51 +0400 |
Daniil Alexeyevsky |
Debugged utils/markup_to_file; some bugs may still be there |
| Tue, 07 Feb 2012 15:38:22 +0400 |
Daniil Alexeyevsky |
Marked utils/markup_to_file.py as executable |
| Sun, 05 Feb 2012 15:07:38 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Sun, 05 Feb 2012 15:07:35 +0400 |
Daniil Alexeyevsky |
muscle removed flag -stable, which we anyhow don't rely upon; removed use of the flag in processors.Muscle |
| Wed, 25 Jan 2012 13:30:37 +0400 |
Boris Nagaev |
Backed out changeset 841c47a94c9e |
| Wed, 25 Jan 2012 00:37:52 +0400 |
Boris Nagaev |
blocks3d/wt: add abstract block (rus and eng) |
| Tue, 24 Jan 2012 22:59:54 +0400 |
Boris Nagaev |
blocks3d/wt: add reference to the Russian Foundation for Basic Research |
| Mon, 19 Dec 2011 21:52:02 +0400 |
Daniil Alexeyevsky |
Clean rewrite of Makefiles for tests, downloading test alignments |
| Mon, 19 Dec 2011 21:43:42 +0400 |
Daniil Alexeyevsky |
Fixed typing bug in allpy.base.Alignment._append_columns, which caused some tests on realigning to fail |
| Thu, 15 Dec 2011 12:31:07 +0300 |
Boris Nagaev |
blocks3d-wt: add an example of an alignment for input for the program |
| Wed, 14 Dec 2011 22:15:48 +0400 |
Daniil Alexeyevsky |
Bumped Debian release number1.4.0 |
| Wed, 14 Dec 2011 21:09:28 +0400 |
Daniil Alexeyevsky |
Fix permissions for /var/run/wt/ for blocks3d-wt1.4.0 |
| Wed, 14 Dec 2011 19:45:57 +0300 |
Daniil Alexeyevsky |
Recorded changes in debian/changelog (not all of them, regretfully)1.4.0 |
| 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)1.4.0 |
| Wed, 02 Nov 2011 19:44:22 +0300 |
Daniil Alexeyevsky |
Debian changelog entry for previous commit1.4.0 |
| Wed, 02 Nov 2011 19:42:48 +0300 |
Daniil Alexeyevsky |
Fixed symlink in blocks3d debian package1.4.0 |
| Thu, 13 Oct 2011 16:28:26 +0400 |
Daniil Alexeyevsky |
Rebuilt blocks3d-wt with newer wt1.4.0 |
| Thu, 21 Jul 2011 14:23:12 +0400 |
Daniil Alexeyevsky |
Removed some of downloaded files fomr blocks3d/wt (see #93)1.4.0 |
| Wed, 14 Dec 2011 22:05:00 +0400 |
Daniil Alexeyevsky |
Removed tag 1.4.0 |
| Wed, 14 Dec 2011 22:04:39 +0400 |
Daniil Alexeyevsky |
Removed tag 1.4.01.4.0 |
| Wed, 20 Jul 2011 19:17:03 +0400 |
Daniil Alexeyevsky |
Added call to blocks3d-www makefile target to debian package building rules (see #62)1.4.0 |
| Wed, 20 Jul 2011 19:09:31 +0400 |
Daniil Alexeyevsky |
Added blocks3d javascript builder target to the global Makefile (closes #62)1.4.0 |
| Wed, 14 Dec 2011 21:09:28 +0400 |
Daniil Alexeyevsky |
Fix permissions for /var/run/wt/ for blocks3d-wt |
| 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 |
