ec99e8cbec249db528cd6a42505be9ffe77e2b06 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/1417218a9fe10fa4d971861c637211a5e02048fb 1417218a9fe10fa4d971861c637211a5e02048fb 2009-12-21T20:11:24-08:00 2009-12-21T14:50:55-08:00 NexusIO: parse and write Bio.Tree.Newick objects Still depends on the original Nexus parser, then converts to the Bio.Tree object hierarchy bdf4edc05d9ba55e01345b50a69a32b2b15d4651 Eric Talevich eric.talevich@gmail.com 0afd9dc319cc98944d14d323d5bc7a294254cc27 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/ec99e8cbec249db528cd6a42505be9ffe77e2b06 ec99e8cbec249db528cd6a42505be9ffe77e2b06 2009-12-21T20:11:23-08:00 2009-12-21T14:45:46-08:00 Newick(IO): removed NH-prefix from class names Made the shim class (_Shim) protected 9bb44f26cb4422443c7fa243e22fafff7b5b0039 Eric Talevich eric.talevich@gmail.com d48a26aa97a958fc64d675498bba2b9f6f0c5952 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/0afd9dc319cc98944d14d323d5bc7a294254cc27 0afd9dc319cc98944d14d323d5bc7a294254cc27 2009-12-21T20:11:01-08:00 2009-12-20T22:55:37-08:00 BaseTree: reorg methods in TreeMixin b3693dd7d5b5144a614e97be10eb2c288ae9e53b Eric Talevich eric.talevich@gmail.com d28f5e312e5956a311bde781a3f654e8535e0be3 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/d48a26aa97a958fc64d675498bba2b9f6f0c5952 d48a26aa97a958fc64d675498bba2b9f6f0c5952 2009-12-08T13:48:28-08:00 2009-12-08T13:48:28-08:00 Tree: renamed Subtree.label to Subtree.name Updated derivatives -- some voodoo with properties went away 3fb5f34e5f402de0cec69088cbec3e10d723e92e Eric Talevich eric.talevich@gmail.com 6508ff94515f3a292dc193ce3b1254e54228c0df Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/d28f5e312e5956a311bde781a3f654e8535e0be3 d28f5e312e5956a311bde781a3f654e8535e0be3 2009-12-07T12:35:53-08:00 2009-12-07T12:35:53-08:00 TreeIO: NewickIO now produces Bio.Tree.Newick objects 5b63ff259e380b7cfcc72ce18688f7b0375532f1 Eric Talevich eric.talevich@gmail.com 4f77d1d8d3c7c95e6a94ca49a28a6f1d19997fc3 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/6508ff94515f3a292dc193ce3b1254e54228c0df 6508ff94515f3a292dc193ce3b1254e54228c0df 2009-12-07T12:24:26-08:00 2009-12-07T12:09:28-08:00 Tree: cleaned up Newick classes a little 6f23360a8e9896bf327fb42d22ee5f62234c7a6e Eric Talevich eric.talevich@gmail.com 7c9f5a5781bb14121ff0076bff9d752919d0dd8b Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/4f77d1d8d3c7c95e6a94ca49a28a6f1d19997fc3 4f77d1d8d3c7c95e6a94ca49a28a6f1d19997fc3 2009-12-04T10:13:21-08:00 2009-12-04T10:08:14-08:00 BaseTree: removed PhyloDB stuff 822fe204b98edaf2271629cc31ec9859387c32a0 Eric Talevich eric.talevich@gmail.com d165dc8e32d1a3cff9a174a9a278821e6bf0c4d3 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/7c9f5a5781bb14121ff0076bff9d752919d0dd8b 7c9f5a5781bb14121ff0076bff9d752919d0dd8b 2009-12-04T10:12:57-08:00 2009-12-04T09:45:01-08:00 Tree: Changed Node to Subtree, created TreeMixin Tree has global phylogeny info, Subtree has topology and node data. There are no nodes, only subtrees and their data. bb30514e1d83057b803cd658dbe23261e65eb629 Eric Talevich eric.talevich@gmail.com b3d643e140144f913c830e1cd8dc1611477aafbe Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/d165dc8e32d1a3cff9a174a9a278821e6bf0c4d3 d165dc8e32d1a3cff9a174a9a278821e6bf0c4d3 2009-12-04T06:49:53-08:00 2009-12-04T06:49:53-08:00 PhyloXMLIO: renamed the BaseTree.PhyloXML import to PX (Calling it Tree was bad for searching and error-prone.) 1b34f48d47cbfede01392dbfb076e73bab21b56b Eric Talevich eric.talevich@gmail.com f92d026c560f5bb194202c8e29de0058543ae70f f3e58fe6003a5ccecc1427638e61c5c4b5cc7775 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/b3d643e140144f913c830e1cd8dc1611477aafbe b3d643e140144f913c830e1cd8dc1611477aafbe 2009-11-20T12:55:06-08:00 2009-11-20T12:55:06-08:00 Merge branch 'master' into phyloxml 25c864f2e19f393d89ad316ec68dfd7d9432cd67 Eric Talevich eric.talevich@gmail.com 394ab1317367e702fc7c23e640600f1d340857f7 62a436932d330e5b3c40d3d6c457356b7a23f6fe Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/f3e58fe6003a5ccecc1427638e61c5c4b5cc7775 f3e58fe6003a5ccecc1427638e61c5c4b5cc7775 2009-11-20T12:54:45-08:00 2009-11-20T12:54:45-08:00 Merge branch 'master' of git://github.com/biopython/biopython 9a87a8d1178d0c153a762d2f4f5c1854ac723aee Eric Talevich eric.talevich@gmail.com ace4d47f5898d2e8c308db313843c904e8d0ad36 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/f92d026c560f5bb194202c8e29de0058543ae70f f92d026c560f5bb194202c8e29de0058543ae70f 2009-11-20T12:53:21-08:00 2009-11-20T12:53:21-08:00 TreeIO: copied Nexus.Trees parser into NewickIO 5407258efa082b141e1da88d1e7db5d9c6696670 Eric Talevich eric.talevich@gmail.com df77c72cf66f349137a921c2d977b3358b778e07 Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/ace4d47f5898d2e8c308db313843c904e8d0ad36 ace4d47f5898d2e8c308db313843c904e8d0ad36 2009-11-20T12:26:25-08:00 2009-11-20T12:26:25-08:00 Tree: renamed findall to find_all & updated everywhere Also implemented find_clades (the clades corresponding to each deeper attribute found in a search) and _function_matcher. 6d69f089af8e5b7fbc6adbeb7cb46e6a78ab95b3 Eric Talevich eric.talevich@gmail.com 27d118df8776934b2299a777eb53f049c4befa8e Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/df77c72cf66f349137a921c2d977b3358b778e07 df77c72cf66f349137a921c2d977b3358b778e07 2009-11-20T12:24:47-08:00 2009-11-20T12:24:47-08:00 PhyloXML: fixed iteration behavior in Phylogeny -- better 210171ac883f469af92bd416ed3a1c74bc6f1d12 Eric Talevich eric.talevich@gmail.com e0c560f017f9971e8e57fd5e76bbabfbef1a5baf Eric Talevich eric.talevich@gmail.com http://github.com/etal/biopython/commit/27d118df8776934b2299a777eb53f049c4befa8e 27d118df8776934b2299a777eb53f049c4befa8e 2009-11-20T12:12:54-08:00 2009-11-20T12:12:54-08:00 PhyloXML: Updated BranchColor color names, RGB values. Source: HTML spec, matplotlib color definitions. 1a2c70accc9a356955f784fe6c00fa267a23d9ef Eric Talevich eric.talevich@gmail.com fa5e1bea78eed472774acd0e76e1cf8e6ce63c2d Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/62a436932d330e5b3c40d3d6c457356b7a23f6fe 62a436932d330e5b3c40d3d6c457356b7a23f6fe 2009-11-20T07:48:27-08:00 2009-11-20T07:48:27-08:00 More doctests in Bio/Seq.py 9a87a8d1178d0c153a762d2f4f5c1854ac723aee Peter p.j.a.cock@googlemail.com 821cc9672d517d82b339a45b2759224730010174 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/fa5e1bea78eed472774acd0e76e1cf8e6ce63c2d fa5e1bea78eed472774acd0e76e1cf8e6ce63c2d 2009-11-20T04:23:45-08:00 2009-11-20T04:23:45-08:00 Include new Bio.SeqFeature doctests in test suite 0e6c0e10d1fb88311e76377f4151c83cb61322a4 Peter p.j.a.cock@googlemail.com c5742ca95a66535b1db4c543f5c701f1c1f8dd83 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/821cc9672d517d82b339a45b2759224730010174 821cc9672d517d82b339a45b2759224730010174 2009-11-20T04:22:23-08:00 2009-11-20T04:22:23-08:00 Basic doctests for Bio.SeqFeature, and checking strand and location arguments 6019eb10ba59742265f9e1d8b483351de7c4badd Peter p.j.a.cock@googlemail.com 062cf979cfa1c68e716102d509169349515d0a1d Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/c5742ca95a66535b1db4c543f5c701f1c1f8dd83 c5742ca95a66535b1db4c543f5c701f1c1f8dd83 2009-11-19T03:06:31-08:00 2009-11-19T03:06:31-08:00 Adding a few PMC associated DTD files, http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/dtd/pmc-1.dtd and http://www.pubmedcentral.nih.gov/pmcdoc/dtd/nlm_lib/articleset/nlm-articleset-2.0.dtd 79fc5fd3df3807d3f8c805fcd8bce982d341ce9f Peter p.j.a.cock@googlemail.com 1c1974490f804cb0d204dfba94bb8e497d316924 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/062cf979cfa1c68e716102d509169349515d0a1d 062cf979cfa1c68e716102d509169349515d0a1d 2009-11-18T09:18:42-08:00 2009-11-18T09:18:42-08:00 Parse atom element field in PDB files (Bug 2495) edfce50881061531a1b49d1714b7a9c49c42d8e3 Peter p.j.a.cock@googlemail.com e5afce76f6c8214714102646fb8f14daa6f49202 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/1c1974490f804cb0d204dfba94bb8e497d316924 1c1974490f804cb0d204dfba94bb8e497d316924 2009-11-18T09:07:06-08:00 2009-11-18T09:07:06-08:00 Adding a small real PDB file containing some HETATM lines for use in unit tests dc3400df4b4230bca027f67abf7cb35188c944fe Peter p.j.a.cock@googlemail.com c779160512ad614bc801b0895a2157a56d19b2cc Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/e5afce76f6c8214714102646fb8f14daa6f49202 e5afce76f6c8214714102646fb8f14daa6f49202 2009-11-18T05:19:14-08:00 2009-11-18T05:19:14-08:00 Unit test and fix for SeqFeature locations in new SeqRecord __radd__ method d304196cc49f174038dbdc0d303bed35ee928260 Peter p.j.a.cock@googlemail.com ecd7698fce4518754e9c6a3e1cf88a6815d86d68 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/c779160512ad614bc801b0895a2157a56d19b2cc c779160512ad614bc801b0895a2157a56d19b2cc 2009-11-18T04:36:38-08:00 2009-11-18T04:36:38-08:00 Basic unit test for SeqRecord slicing with a full length source feature ef1c61421b8ad1689cd48612dedaf7d9b6337144 Peter p.j.a.cock@googlemail.com 4dc83f186beab0d54f65992bb0ebecea78c48ffc Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/ecd7698fce4518754e9c6a3e1cf88a6815d86d68 ecd7698fce4518754e9c6a3e1cf88a6815d86d68 2009-11-18T04:17:39-08:00 2009-11-18T04:17:39-08:00 Fixed SeqRecord slicing for SeqFeature with OneOfPosition a612974429e687ea206deb9f82be8152ac234350 Peter p.j.a.cock@googlemail.com 197d69b8f2efcd6f33fedbc20833189bdbcca36d mdehoon mdehoon@anx136.genome.gsc.riken.jp http://github.com/etal/biopython/commit/4dc83f186beab0d54f65992bb0ebecea78c48ffc 4dc83f186beab0d54f65992bb0ebecea78c48ffc 2009-11-17T00:12:23-08:00 2009-11-17T00:12:23-08:00 Adding final tests for the MAST parser f86809849c21655e99fdada812ab55d54c1e7117 mdehoon mdehoon@anx136.genome.gsc.riken.jp 5f49cfe4ab46073a737e70a00eb7af2cb1504f95 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/197d69b8f2efcd6f33fedbc20833189bdbcca36d 197d69b8f2efcd6f33fedbc20833189bdbcca36d 2009-11-16T10:00:23-08:00 2009-11-16T10:00:23-08:00 Working on standalone BLAST section of the Tutorial 12e6e90baf857b745f3e1446ef577340cf20b423 Peter p.j.a.cock@googlemail.com 72d3a0606bb8289b6bca38f0135355d879143a5a Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/5f49cfe4ab46073a737e70a00eb7af2cb1504f95 5f49cfe4ab46073a737e70a00eb7af2cb1504f95 2009-11-16T09:22:25-08:00 2009-11-16T09:22:25-08:00 Starting work on the BLAST chapter of the tutorial. Moving online section to the start (simpler for beginners) ae73335daaf5a9187103d9a216d44bfb27fd5200 Peter p.j.a.cock@googlemail.com 98982f29418265c4e79319e8d8b21ea2a236140a Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/72d3a0606bb8289b6bca38f0135355d879143a5a 72d3a0606bb8289b6bca38f0135355d879143a5a 2009-11-16T07:00:26-08:00 2009-11-16T07:00:26-08:00 Should have all BLAST+ command line arguments supported now, except soft_masking and use_index where it is unclear from the documentation if they should be a 'switch' or an 'option' taking a boolean argument f05eaf0c787d5d53487714a762cac040cfdcc09e Peter p.j.a.cock@googlemail.com 7499c238eb2ab165781baaeaa369907f0dbf7d2d Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/98982f29418265c4e79319e8d8b21ea2a236140a 98982f29418265c4e79319e8d8b21ea2a236140a 2009-11-16T06:40:34-08:00 2009-11-16T06:40:34-08:00 Adding more missing NCBI BLAST+ options (guided by the new unit test), should be everything except for some blastn options e8e788a5cc8e98e4dca5b757e0605290374b76c9 Peter p.j.a.cock@googlemail.com e41f912625f2a192735434c5771d9b147b8fa300 Peter p.j.a.cock@googlemail.com http://github.com/etal/biopython/commit/7499c238eb2ab165781baaeaa369907f0dbf7d2d 7499c238eb2ab165781baaeaa369907f0dbf7d2d 2009-11-16T06:28:19-08:00 2009-11-16T06:28:19-08:00 Adding more missing NCBI BLAST+ options (guided by the new unit test) d4993e47c424f3612d654b938f4c27f7fb4c6a21 Peter p.j.a.cock@googlemail.com