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https://github.com/jhbadger/APIS
05 April 2024, 21:57:11 UTC
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Revision Author Date Message Commit Date
66a20cb Jonathan Badger 03 April 2015, 14:00:24 UTC first version that can use refseq 03 April 2015, 14:00:24 UTC
1925896 Jonathan Badger 13 March 2015, 23:45:33 UTC removed extra ZFILE from jsonQuery 13 March 2015, 23:45:33 UTC
828e640 Jonathan Badger 13 January 2015, 20:38:11 UTC removed reannotation (not working) 13 January 2015, 20:38:11 UTC
1567d61 Jonathan Badger 26 November 2014, 18:47:22 UTC allow saving alignments to be optional 26 November 2014, 18:47:22 UTC
32f0b7c Jonathan Badger 26 November 2014, 18:30:14 UTC fix cases with peptide names with slashes 26 November 2014, 18:30:14 UTC
bba335c Jonathan Badger 13 November 2014, 19:07:00 UTC output name is up to .json 13 November 2014, 19:07:00 UTC
bcf974b Jonathan Badger 13 November 2014, 18:45:12 UTC utility script to breakup json file into pieces 13 November 2014, 18:45:12 UTC
83d4bcc Jonathan Badger 13 November 2014, 18:22:49 UTC only print taxon_id if one assigned 13 November 2014, 18:22:49 UTC
3ee0dbc Jonathan Badger 13 November 2014, 00:13:36 UTC ignore first level of classification if empty 13 November 2014, 00:13:36 UTC
1e6f9a4 Jonathan Badger 12 November 2014, 22:03:13 UTC more less specific in reclassifyApis 12 November 2014, 22:03:13 UTC
19fc2ab Jonathan Badger 12 November 2014, 20:16:14 UTC classify higher node if taxonomy of current node not found 12 November 2014, 20:16:14 UTC
7364c13 Jonathan Badger 05 November 2014, 20:06:11 UTC reclassifyAPIS 05 November 2014, 20:06:11 UTC
8af1325 Jonathan Badger 19 March 2014, 19:15:45 UTC Unclassfied category 19 March 2014, 19:15:45 UTC
bda785a Jonathan Badger 19 March 2014, 17:45:00 UTC Merge branch 'master' of https://github.com/jhbadger/APIS 19 March 2014, 17:45:00 UTC
13776ce Jonathan Badger 19 March 2014, 17:44:39 UTC zeroes in excel spreadsheet 19 March 2014, 17:44:39 UTC
24d130e Jonathan Badger 12 March 2014, 19:52:51 UTC apisPie update Merge branch 'master' of jbadger2-osx:Projects/APIS 12 March 2014, 19:52:51 UTC
a5d9b82 Jonathan Badger 12 March 2014, 19:45:49 UTC skip taxa with no taxonomy 12 March 2014, 19:45:49 UTC
c84e9a8 Jonathan Badger 05 March 2014, 01:12:21 UTC Merge branch 'master' of https://github.com/jhbadger/APIS 05 March 2014, 01:12:21 UTC
dd7c29c Jonathan Badger 05 March 2014, 01:12:02 UTC excel in apisPie 05 March 2014, 01:12:02 UTC
5e05ae3 Jonathan Badger 04 March 2014, 02:04:11 UTC Merge branch 'master' of https://github.com/jhbadger/APIS 04 March 2014, 02:04:11 UTC
47f0578 Jonathan Badger 04 March 2014, 02:03:59 UTC fix . in dataset 04 March 2014, 02:03:59 UTC
9a8e2ca Jonathan Badger 04 March 2014, 01:58:22 UTC fix . in dataset 04 March 2014, 01:58:22 UTC
278da3a Jonathan Badger 03 March 2014, 07:55:08 UTC apisPie 03 March 2014, 07:55:08 UTC
61fb085 Jonathan Badger 02 March 2014, 22:55:36 UTC handle Ion Torrent Reads 02 March 2014, 22:55:36 UTC
a01e6b7 Jonathan Badger 31 January 2014, 19:26:10 UTC working new grid system 31 January 2014, 19:26:10 UTC
825e892 Jonathan Badger 31 January 2014, 19:18:27 UTC New Grid system 31 January 2014, 19:18:27 UTC
a9db6d6 Jonathan Badger 30 December 2013, 17:39:30 UTC allowed split datanases in apisTimeLogicBlast 30 December 2013, 17:39:30 UTC
496dc92 Jonathan Badger 27 December 2013, 16:59:53 UTC fixed array issue for apisTimeLogicBlast 27 December 2013, 16:59:53 UTC
3d051fe Jonathan Badger 19 December 2013, 23:52:22 UTC Grid APIS now working again 19 December 2013, 23:52:22 UTC
3dc748d Jonathan Badger 19 December 2013, 22:57:22 UTC goxed fastacmd error 19 December 2013, 22:57:22 UTC
08cb68b Jonathan Badger 19 December 2013, 22:33:21 UTC don't report errors in fastacmd 19 December 2013, 22:33:21 UTC
919a2d4 Jonathan Badger 19 December 2013, 22:28:34 UTC handle multiple taxonomies and databases 19 December 2013, 22:28:34 UTC
a2e5789 Jonathan Badger 12 December 2013, 22:37:49 UTC new source base 12 December 2013, 22:37:49 UTC
7d5f8ad Jonathan Badger 10 January 2013, 19:39:02 UTC fastercsv rather than csb for 1.8 10 January 2013, 19:39:02 UTC
be4b986 Jonathan Badger 08 January 2013, 21:30:48 UTC use fastercsv in findTrees 08 January 2013, 21:30:48 UTC
5a10ba2 Jonathan Badger 08 January 2013, 21:29:07 UTC use fastcsv in findTrees 08 January 2013, 21:29:07 UTC
9817719 Jonathan Badger 20 December 2012, 23:36:34 UTC removed 1.9.2 requirement 20 December 2012, 23:36:34 UTC
4b96d77 Jonathan Badger 14 September 2012, 17:06:30 UTC Allow phylometarep format 14 September 2012, 17:06:30 UTC
15649ea Jonathan Badger 13 September 2012, 18:58:26 UTC have separate uniq step in mrerge blast to remove redundant lines 13 September 2012, 18:58:26 UTC
dd6f9b7 Jonathan Badger 13 September 2012, 17:57:41 UTC Changes to work with multi-blast from phylometarep 13 September 2012, 17:57:41 UTC
5a96fc2 Jonathan Badger 15 August 2012, 19:44:52 UTC allow null uri 15 August 2012, 19:44:52 UTC
55ae7f7 Jonathan Badger 15 August 2012, 19:41:26 UTC mods for phylodb 1.05 15 August 2012, 19:41:26 UTC
a9587e8 Jonathan Badger 31 July 2012, 21:03:56 UTC mysql server gone away better handling 31 July 2012, 21:03:56 UTC
1a80afa Jonathan Badger 03 July 2012, 20:01:31 UTC check to see if support progs exist 03 July 2012, 20:01:31 UTC
f0d5173 Jonathan Badger 03 July 2012, 17:03:10 UTC check for apis version 03 July 2012, 17:03:10 UTC
2221328 Jonathan Badger 09 May 2012, 17:05:55 UTC Linux version of support bin 09 May 2012, 17:05:55 UTC
0bdee28 Jonathan Badger 08 May 2012, 22:58:30 UTC remove dependency on environmental variables for paths 08 May 2012, 22:58:30 UTC
4e29d11 Jonathan Badger 20 March 2012, 16:48:27 UTC normal metarep, not phylo-metarep 20 March 2012, 16:48:27 UTC
e06ae34 Jonathan Badger 20 March 2012, 16:01:45 UTC metaLink or ncbi link as needed 20 March 2012, 16:01:45 UTC
31b7a2e Jonathan Badger 20 March 2012, 15:48:39 UTC metaLink link to metarep 20 March 2012, 15:48:39 UTC
656cf38 Jonathan Badger 23 February 2012, 23:46:55 UTC add close at start of apisRun to free connection 23 February 2012, 23:46:55 UTC
7f86621 Jonathan Badger 23 February 2012, 22:46:59 UTC fixed empty homolog file problem 23 February 2012, 22:46:59 UTC
45dc352 Jonathan Badger 23 February 2012, 21:25:05 UTC =, not == in sql 23 February 2012, 21:25:05 UTC
fd896f6 Jonathan Badger 23 February 2012, 21:18:44 UTC have unprocessed flag 23 February 2012, 21:18:44 UTC
2fa8736 Jonathan Badger 23 February 2012, 21:06:20 UTC close database connection after every query to hopefully improve grid performance 23 February 2012, 21:06:20 UTC
bc4f69f Jonathan Badger 23 February 2012, 19:26:55 UTC added separate time logic blast script 23 February 2012, 19:26:55 UTC
a7fe870 Jonathan Badger 15 February 2012, 01:00:30 UTC added rescue for root node bootstrap 15 February 2012, 01:00:30 UTC
b6595db Jonathan Badger 07 February 2012, 01:19:38 UTC handle empty alignment 07 February 2012, 01:19:38 UTC
cb5c01b Jonathan Badger 04 February 2012, 02:33:21 UTC skipTree option 04 February 2012, 02:33:21 UTC
eb16573 Jonathan Badger 03 February 2012, 18:42:43 UTC removed redundant scripts 03 February 2012, 18:42:43 UTC
101c6c0 Jonathan Badger 03 February 2012, 18:42:11 UTC supplementary scripts now working 03 February 2012, 18:42:11 UTC
5be4eac Jonathan Badger 03 February 2012, 18:03:09 UTC fixed wrong # of args in createClassification 03 February 2012, 18:03:09 UTC
fa8fae4 Jonathan Badger 03 February 2012, 00:33:27 UTC createApisCSV works 03 February 2012, 00:33:27 UTC
fc883a7 Jonathan Badger 01 February 2012, 19:28:46 UTC timelogic database find 01 February 2012, 19:28:46 UTC
f65da22 Jonathan Badger 01 February 2012, 16:55:06 UTC restore rescue to processTree 01 February 2012, 16:55:06 UTC
433c274 Jonathan Badger 01 February 2012, 16:31:30 UTC use proteindb name for timelogic 01 February 2012, 16:31:30 UTC
ff9f351 Jonathan Badger 01 February 2012, 16:23:01 UTC fixed tax string in ApisDB 01 February 2012, 16:23:01 UTC
f456057 Jonathan Badger 31 January 2012, 23:41:41 UTC APIS using phylodb 1.04 first version 31 January 2012, 23:41:41 UTC
1979ff5 Jonathan Badger 14 October 2011, 23:32:34 UTC propagate database option to grid jobs 14 October 2011, 23:32:34 UTC
419be3b Jonathan Badger 14 October 2011, 22:47:47 UTC allow choice of protein database in APIS 14 October 2011, 22:47:47 UTC
317b0fc Jonathan Badger 14 October 2011, 20:47:53 UTC option to avoid recreating existing reports in createApisCSV 14 October 2011, 20:47:53 UTC
581c2dc Jonathan Badger 12 October 2011, 20:38:34 UTC remove duplicates 12 October 2011, 20:38:34 UTC
4650c0f Jonathan Badger 12 October 2011, 18:37:43 UTC improved blast query for top hit 12 October 2011, 18:37:43 UTC
e4ac75c Jonathan Badger 11 October 2011, 22:42:45 UTC remove redundant header 11 October 2011, 22:42:45 UTC
0dd8814 Jonathan Badger 11 October 2011, 22:40:35 UTC more efficient blast full in createApisCSV 11 October 2011, 22:40:35 UTC
0dc247c Jonathan Badger 10 October 2011, 19:37:26 UTC add identity, coverage to blast report in createApisCSV 10 October 2011, 19:37:26 UTC
558afd7 Jonathan Badger 09 October 2011, 14:42:03 UTC fix colons screwing up trees 09 October 2011, 14:42:03 UTC
d83d638 Jonathan Badger 09 October 2011, 14:00:37 UTC timelogic blast 09 October 2011, 14:00:37 UTC
de35b6b Jonathan Badger 08 October 2011, 01:06:41 UTC improved configuration 08 October 2011, 01:06:41 UTC
ea71714 Jonathan Badger 07 October 2011, 22:46:04 UTC configuration file of host 07 October 2011, 22:46:04 UTC
0a6233b Jonathan Badger 07 October 2011, 21:32:08 UTC fixed insert issue 07 October 2011, 21:32:08 UTC
a77e8d5 Jonathan Badger 07 October 2011, 20:00:09 UTC fix annotation 07 October 2011, 20:00:09 UTC
f1b1d36 Jonathan Badger 07 October 2011, 19:34:31 UTC test version of new apis 07 October 2011, 19:34:31 UTC
86d250a Jonathan Badger 06 October 2011, 20:09:15 UTC count method 06 October 2011, 20:09:15 UTC
147040b Jonathan Badger 06 October 2011, 20:02:40 UTC WebAPIS 06 October 2011, 20:02:40 UTC
62e3938 Jonathan Badger 06 October 2011, 19:30:21 UTC moved to sql for efficency 06 October 2011, 19:30:21 UTC
1498121 Jonathan Badger 04 October 2011, 19:55:41 UTC moved favicon 04 October 2011, 19:55:41 UTC
382d504 Jonathan Badger 04 October 2011, 19:33:57 UTC icon 04 October 2011, 19:33:57 UTC
18b6d71 Jonathan Badger 04 October 2011, 18:35:20 UTC to_s before quite 04 October 2011, 18:35:20 UTC
9ab446d Jonathan Badger 04 October 2011, 16:06:39 UTC quoting of single quotes 04 October 2011, 16:06:39 UTC
25f6f48 Jonathan Badger 03 October 2011, 20:54:39 UTC fixed relaxed classification 03 October 2011, 20:54:39 UTC
f988e78 Jonathan Badger 22 September 2011, 23:53:59 UTC allow taxonomies without spaces 22 September 2011, 23:53:59 UTC
8fc1ad4 Jonathan Badger 21 September 2011, 21:45:59 UTC Merge branch 'master' of github.com:jhbadger/APIS 21 September 2011, 21:45:59 UTC
b168517 Jonathan Badger 21 September 2011, 21:45:13 UTC active_record apisPie, createApisCSV 21 September 2011, 21:45:13 UTC
542fe43 Jonathan Badger 16 September 2011, 19:39:48 UTC fixed parsing of RAST scaffolds 16 September 2011, 19:39:48 UTC
c22a7ca Jonathan Badger 30 August 2011, 22:20:23 UTC only add database if not there already 30 August 2011, 22:20:23 UTC
66a316e Jonathan Badger 26 August 2011, 00:21:35 UTC Active Record 26 August 2011, 00:21:35 UTC
2e8f7be Jonathan Badger 17 August 2011, 20:27:45 UTC fixed typo 17 August 2011, 20:27:45 UTC
cedb1bb Jonathan Badger 17 August 2011, 19:32:14 UTC remove apisRun, _input from dataset name on grid 17 August 2011, 19:32:14 UTC
67d3efe Jonathan Badger 17 August 2011, 17:49:20 UTC don't have .pep on input files grid doesn't like it 17 August 2011, 17:49:20 UTC
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