| age |
author |
description |
| Sun, 03 Jun 2012 12:09:41 +0400 |
Daniil Alexeyevsky |
Added meta-processor `FixNamesAndOrder`; called from `Needle` and `Muscle` (closes #134) |
| Sat, 02 Jun 2012 22:33:50 +0400 |
Daniil Alexeyevsky |
processors.Needle: also check that sequence name is not empty (needle fails on those too) |
| Fri, 01 Jun 2012 14:32:07 +0400 |
Daniil Alexeyevsky |
Silenced all known noisy points in allpy |
| Wed, 30 May 2012 13:35:04 +0400 |
Daniil Alexeyevsky |
Bugfixed the previous commit (decency verification), (see #98) |
| Mon, 19 Mar 2012 13:52:56 +0400 |
Boris Nagaev |
Merged utils, pair_cores, blocks3d and geometrical-core from 9ae23 into 1.4.21.4.2 |
| Fri, 16 Mar 2012 16:45:00 +0400 |
Daniil Alexeyevsky |
Merged allpy & tests from 1.4.0 into 1.4.21.4.2 |
| 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 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 |
| 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 |
| Mon, 28 Nov 2011 18:33:25 +0300 |
Daniil Alexeyevsky |
Fixed bug in processors: used Block class for reading alignment file. |
| Mon, 21 Nov 2011 18:05:14 +0300 |
Daniil Alexeyevsky |
processors.Needle does not yet allow : in sequence names |
| Tue, 08 Nov 2011 19:12:37 +0300 |
Daniil Alexeyevsky |
allpy.processor.ExternalCommand: close file descriptors from temporary files |
| Tue, 12 Jul 2011 16:16:08 +0400 |
Daniil Alexeyevsky |
allpy.processors: made Muscle() silent |
| Wed, 25 May 2011 20:25:32 +0400 |
Daniil Alexeyevsky |
Added sectioning comments to allpy.processors |
| Wed, 25 May 2011 19:49:12 +0400 |
Daniil Alexeyevsky |
allpy.processors: cleaner reimplementation of remove_gaps option in Muscle |
| Wed, 25 May 2011 19:46:20 +0400 |
Daniil Alexeyevsky |
allpy.processors: code cleanup, added more docstrings |
| Tue, 24 May 2011 22:12:57 +0400 |
Daniil Alexeyevsky |
Implemented processor.FixOrder and processor.BypassEmpty as processors instead of hacky fix_order and fix_empty helper functions |
| Fri, 20 May 2011 13:35:09 +0400 |
Daniil Alexeyevsky |
Code cleanup allpy.processors: removed ExternalCommand.to_file; renamed no_gaps to remove_gaps in Muscle |
| Thu, 19 May 2011 22:13:56 +0400 |
Daniil Alexeyevsky |
Implemented processors.Needle; hacky and dirty, just like the rest of the module |
| Thu, 17 Mar 2011 16:56:48 +0300 |
boris (kodomo) |
processors: add no_gaps parameter to Muscle processor |
| Mon, 28 Feb 2011 22:40:16 +0300 |
Daniil Alexeyevsky |
allpy.processors: make temporary files named |
| Mon, 28 Feb 2011 21:17:41 +0300 |
Daniil Alexeyevsky |
Reimplemented flush(direction) as processor1.2.0 |
| Tue, 15 Feb 2011 22:47:34 +0300 |
Daniil Alexeyevsky |
Simple logical bug in processors.fix_missing |
| Tue, 15 Feb 2011 22:32:14 +0300 |
Daniil Alexeyevsky |
processors: muscle removes empty rows from output; fix this by adding necessary empty sequences to output block |
| Tue, 15 Feb 2011 22:16:35 +0300 |
Daniil Alexeyevsky |
processors: Muscle() now takes care of restoring sequence ordering after command run |
| Tue, 01 Feb 2011 17:11:33 +0300 |
boris |
fixed bugs; usecase1.py works (see #23) (see #1) |
| Tue, 01 Feb 2011 00:20:24 +0300 |
boris |
fix base processor (refs #23) |
| Mon, 31 Jan 2011 23:39:26 +0300 |
boris |
Implemented base processor for realignments (see #23) |
| Wed, 26 Jan 2011 21:34:36 +0300 |
Daniil Alexeyevsky |
Implemented stub of allpy.processors module. (see #23) |
