b38513681039a6b39033434e631b6a7ce198a50f Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/70c5d4b972f0677c6855f586581729ab16093986 70c5d4b972f0677c6855f586581729ab16093986 2008-10-09T04:16:58-07:00 2008-10-09T04:16:58-07:00 generate_fixtures.rb now produces fixtures for alignment codon costs 2e8148a8424b9e1cabe83d3f9c39482a6dc1473e Michael Barton mail@michaelbarton.me.uk 55e72284a5871cbb8fea955fb825309ebab45fd1 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/b38513681039a6b39033434e631b6a7ce198a50f b38513681039a6b39033434e631b6a7ce198a50f 2008-10-09T04:16:41-07:00 2008-10-09T04:16:41-07:00 Fixtures for alignment codon costs 9300e26233b5ed182a732afa24527f437b594da3 Michael Barton mail@michaelbarton.me.uk 2ae93577d59fe76b4758647733d51cf84aafb53a Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/55e72284a5871cbb8fea955fb825309ebab45fd1 55e72284a5871cbb8fea955fb825309ebab45fd1 2008-10-09T04:16:20-07:00 2008-10-09T04:16:20-07:00 Regenerated fixtures 33f5b68d961402c91ecc8e3ffdf0bc6d877194a5 Michael Barton mail@michaelbarton.me.uk 5e48189023feab2cc2059bee2e068282004ca184 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/2ae93577d59fe76b4758647733d51cf84aafb53a 2ae93577d59fe76b4758647733d51cf84aafb53a 2008-10-09T04:14:17-07:00 2008-10-09T04:14:17-07:00 Set database file logger reference to be absolute 33e5dfccf165c4a0c36b01301a5140176fff834f Michael Barton mail@michaelbarton.me.uk 74a8896375b2406c686414528dda309d3d1b8893 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/5e48189023feab2cc2059bee2e068282004ca184 5e48189023feab2cc2059bee2e068282004ca184 2008-10-09T03:54:59-07:00 2008-10-09T03:54:59-07:00 Repress activerecord migration messages defbe2fbcaf18f9e41607d8cf7a27236bc284905 Michael Barton mail@michaelbarton.me.uk 2aa0bb392b2ccfe680a5bd9f5568c9d89c1a69a8 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/74a8896375b2406c686414528dda309d3d1b8893 74a8896375b2406c686414528dda309d3d1b8893 2008-10-09T03:48:59-07:00 2008-10-09T03:48:59-07:00 Created migration for correlations_by_gene table e5ac55113065158d17040dfcb5b83be5a7bfd1b0 Michael Barton mail@michaelbarton.me.uk c175ca1393b9ca28cf0d9091414815a13d819fdc Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/2aa0bb392b2ccfe680a5bd9f5568c9d89c1a69a8 2aa0bb392b2ccfe680a5bd9f5568c9d89c1a69a8 2008-10-09T03:39:47-07:00 2008-10-09T03:39:47-07:00 Added correlation_by_gene model b7cfc4d590a810425f2677a05c68b5da2cb614ef Michael Barton mail@michaelbarton.me.uk 70b7ccb16f348f7efd798e03fed2681249d3269d Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/c175ca1393b9ca28cf0d9091414815a13d819fdc c175ca1393b9ca28cf0d9091414815a13d819fdc 2008-10-09T02:32:21-07:00 2008-10-09T02:32:21-07:00 Created R script to plot site mutation rate density 6cf672a05d1854a4854f97db4336442177f12680 Michael Barton mail@michaelbarton.me.uk 63ff48384dea4d50aa88a21e52a22701d2ced028 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/70b7ccb16f348f7efd798e03fed2681249d3269d 70b7ccb16f348f7efd798e03fed2681249d3269d 2008-10-09T02:31:10-07:00 2008-10-09T02:31:10-07:00 Removed whitespace e6b91dbb7b061a98d1594b2cb353556509ed9154 Michael Barton mail@michaelbarton.me.uk 6f40b37c8c7a2473cdccfc138b6b1d46f47190ba Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/63ff48384dea4d50aa88a21e52a22701d2ced028 63ff48384dea4d50aa88a21e52a22701d2ced028 2008-10-09T02:29:47-07:00 2008-10-09T02:29:47-07:00 Added script to plot densitiy of codon costs ef6206ed11a834ca356c4a66dcb483b011dea5b6 Michael Barton mail@michaelbarton.me.uk 5b013ef8d72bd08b66aae78d5330871949c1a4bb Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/6f40b37c8c7a2473cdccfc138b6b1d46f47190ba 6f40b37c8c7a2473cdccfc138b6b1d46f47190ba 2008-10-09T02:28:22-07:00 2008-10-09T02:28:22-07:00 Added r script to plot gene cost density 560a85b4c37695d6f1a36b4531dd6717b2a4937d Michael Barton mail@michaelbarton.me.uk 7323a104eb49038475f443ceb58f8a860472e593 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/5b013ef8d72bd08b66aae78d5330871949c1a4bb 5b013ef8d72bd08b66aae78d5330871949c1a4bb 2008-10-09T02:26:46-07:00 2008-10-09T02:26:46-07:00 Average protein cost SQL file now includes standard deviation 84bb862141b0240d5a56555fa4855ba50ff90211 Michael Barton mail@michaelbarton.me.uk 8909334d9227d2455657a82d465d9211c6af94ad Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/7323a104eb49038475f443ceb58f8a860472e593 7323a104eb49038475f443ceb58f8a860472e593 2008-10-09T02:23:52-07:00 2008-10-09T02:23:52-07:00 Created rake task to print sitewise mutation rate data f0f6298b07e5133ec27b697c93b4f4f419ac2f0b Michael Barton mail@michaelbarton.me.uk 8d56877c0ff5d48d37f505874615db4e8aa53815 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/8909334d9227d2455657a82d465d9211c6af94ad 8909334d9227d2455657a82d465d9211c6af94ad 2008-10-09T02:21:33-07:00 2008-10-09T02:21:33-07:00 Created SQL file to print sitewise mutation rate data 1174eb59dc32308589e1ab7d533846f7cb94ef8a Michael Barton mail@michaelbarton.me.uk 29a24f7e9de03b6db491994c3b660bd3d8e1d0d0 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/8d56877c0ff5d48d37f505874615db4e8aa53815 8d56877c0ff5d48d37f505874615db4e8aa53815 2008-10-06T04:06:16-07:00 2008-10-06T04:06:16-07:00 Concat cost and environment together in select for alignment codon costs fcff5ca47eb3417513616a6dbaaf06760e27b642 Michael Barton mail@michaelbarton.me.uk 4856fe9734913d2e4150e0997d5c00b8264a0018 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/29a24f7e9de03b6db491994c3b660bd3d8e1d0d0 29a24f7e9de03b6db491994c3b660bd3d8e1d0d0 2008-10-02T08:26:04-07:00 2008-10-02T08:26:04-07:00 Ignore files in data directories c225951ccd28a77cc30a6ecbe189faff72cf75fb Michael Barton mail@michaelbarton.me.uk 333f16cfc839f9ac19137a02fe883e38c253a142 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/4856fe9734913d2e4150e0997d5c00b8264a0018 4856fe9734913d2e4150e0997d5c00b8264a0018 2008-10-02T08:05:31-07:00 2008-10-02T08:05:31-07:00 Removed datasets from revision control dd5b746cbf5e443f63217d51e0f627e6e8366876 Michael Barton mail@michaelbarton.me.uk 45126b625f17e4a26d091d447364b20849ff1dac 8d794d80182e4d1506fa26289dc9b3e5de05aa42 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/333f16cfc839f9ac19137a02fe883e38c253a142 333f16cfc839f9ac19137a02fe883e38c253a142 2008-10-02T08:03:56-07:00 2008-10-02T08:03:56-07:00 Merge branch 'master' of git@github.com:michaelbarton/cost_in_evolution Conflicts: analysis/003_estimate_amino_acid_frequency_and_cost/r/scripts/plot_gene_costs_density.R helpers/output_from_sql.rb 4f526a003ddb8e9482f7976b73759285ce84e6f0 Michael Barton mail@michaelbarton.me.uk 09a30bbca68c1ff4e57c0718f6552572d6da5aaa Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/45126b625f17e4a26d091d447364b20849ff1dac 45126b625f17e4a26d091d447364b20849ff1dac 2008-10-02T08:01:29-07:00 2008-10-02T07:50:11-07:00 Added script to plot gene costs density dd5b746cbf5e443f63217d51e0f627e6e8366876 Michael Barton mail@michaelbarton.me.uk 3dadc0814f788933aad71d50e5c3e99241b3bfd8 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/09a30bbca68c1ff4e57c0718f6552572d6da5aaa 09a30bbca68c1ff4e57c0718f6552572d6da5aaa 2008-10-02T08:01:29-07:00 2008-10-02T07:44:26-07:00 Updated output_from_sql, no longer stores entire dataset in memory b58ebf453f12a30cc2138eb5e51b16dd6e80155c Michael Barton mail@michaelbarton.me.uk 11bab66f1da6489e7b76c480c462395f03b92995 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/3dadc0814f788933aad71d50e5c3e99241b3bfd8 3dadc0814f788933aad71d50e5c3e99241b3bfd8 2008-10-02T08:01:29-07:00 2008-10-02T07:43:30-07:00 Alignment codon starfish loader uses Alignment as queue rather than alignment codon f4984c697900a9fe2fefa2f162530ab65539c824 Michael Barton mail@michaelbarton.me.uk 82441668b0af4aac46b435246d429f5640cc6d79 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/11bab66f1da6489e7b76c480c462395f03b92995 11bab66f1da6489e7b76c480c462395f03b92995 2008-10-02T08:01:29-07:00 2008-10-02T07:42:34-07:00 Alignment codon uses new + save, rather than create e60b99d459512ed29fdd7720faec2a8a93ba085d Michael Barton mail@michaelbarton.me.uk 3af431367aa68407388015ccb521662bc9b4ae3b Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/82441668b0af4aac46b435246d429f5640cc6d79 82441668b0af4aac46b435246d429f5640cc6d79 2008-10-02T08:01:29-07:00 2008-10-02T07:33:23-07:00 Added spec to ensure correct number of alignment codon costs are created ff4a43bad41ae62417fc5e03e3d445beb75c00e9 Michael Barton mail@michaelbarton.me.uk 5e2d50f54403eb85fb85ba12af2b81547b4d719f Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/3af431367aa68407388015ccb521662bc9b4ae3b 3af431367aa68407388015ccb521662bc9b4ae3b 2008-10-02T08:01:29-07:00 2008-10-02T07:32:38-07:00 Added spec to ensure alignment.alignment_codons association returns expected ffe3ee6fb7f9d4bfca43e5df956d3352f160e69d Michael Barton mail@michaelbarton.me.uk cd0fa35b76474930a3116d50b46a6d82f2392ce1 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/5e2d50f54403eb85fb85ba12af2b81547b4d719f 5e2d50f54403eb85fb85ba12af2b81547b4d719f 2008-10-02T08:01:28-07:00 2008-10-01T10:18:25-07:00 Helper to output data using an SQL statement ca369a12b6bfc6f7ebca7408fabb5937338c9a83 Michael Barton mail@michaelbarton.me.uk b2e3b50e393041919a8c43b1490a73d940062b6c Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/cd0fa35b76474930a3116d50b46a6d82f2392ce1 cd0fa35b76474930a3116d50b46a6d82f2392ce1 2008-10-02T08:01:28-07:00 2008-10-01T10:17:46-07:00 Script to plot average protein cost dataset f324e72330e488878c79406f261ab77c147c9501 Michael Barton mail@michaelbarton.me.uk 11571bcc86254b914ab8589cf54928504433bc36 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/b2e3b50e393041919a8c43b1490a73d940062b6c b2e3b50e393041919a8c43b1490a73d940062b6c 2008-10-02T08:01:28-07:00 2008-09-29T05:42:45-07:00 Added specs to check alignment cost codon validations 3557a67c74dfe9fb82c387761ccd00cfc74adc65 Michael Barton mail@michaelbarton.me.uk 3be84003d7257a9b9fed060ecc687137c2315078 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/11571bcc86254b914ab8589cf54928504433bc36 11571bcc86254b914ab8589cf54928504433bc36 2008-10-02T08:01:28-07:00 2008-09-29T05:32:46-07:00 Added validations for uniqueness and presence of attributes 11552b850940cc7b009efba79d155b72f689cdc7 Michael Barton mail@michaelbarton.me.uk 1f4d37d77e073e8350b44d5bfc033c065cfd2c81 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/8d794d80182e4d1506fa26289dc9b3e5de05aa42 8d794d80182e4d1506fa26289dc9b3e5de05aa42 2008-10-01T10:18:25-07:00 2008-10-01T10:18:25-07:00 Helper to output data using an SQL statement e45c5a6ddbfda03e49398616c645a9c7fc8323f2 Michael Barton mail@michaelbarton.me.uk 44d2127aac6d9f3cff0cfc5686743d72c166ce70 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/1f4d37d77e073e8350b44d5bfc033c065cfd2c81 1f4d37d77e073e8350b44d5bfc033c065cfd2c81 2008-10-01T10:17:46-07:00 2008-10-01T10:17:46-07:00 Script to plot average protein cost dataset aaff523fc11df47fcb0ce356ffd355be67a7ddc0 Michael Barton mail@michaelbarton.me.uk