| Time |
Nick |
Message |
| 00:09 |
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| 04:55 |
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| 04:56 |
pyrimidine |
burp.... good hackathon..... |
| 04:56 |
pyrimidine |
:P |
| 04:56 |
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| 05:57 |
deafferret |
/win 45 |
| 06:39 |
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| 09:11 |
dbolser |
who's hacking? |
| 09:42 |
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| 10:23 |
dbolser |
how come I see 'All tests successful.' in git vsn of bioperl when earlier I see "t/LocalDB/SeqFeature_mysql.t ................. 1/84 DBI connect('database=test','',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217 |
| 10:24 |
dbolser |
" |
| 10:24 |
dbolser |
? |
| 10:34 |
kai |
dunno, I don't run the mysql stuff :) |
| 10:39 |
dbolser |
nobody does, that is part of the problem |
| 10:39 |
dbolser |
but the real problem is why it says "All tests successful" when t/LocalDB/SeqFeature_mysql.t fails |
| 10:39 |
* dbolser |
carefully crafts an email ;-) |
| 10:46 |
dbolser |
I'm suffering brain split |
| 11:28 |
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| 11:51 |
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| 12:18 |
dbolser |
hello |
| 12:28 |
kai |
hm, I wonder how the heck I go about joining all these contigs |
| 12:28 |
dbolser |
kai: in real life or in bioperl? |
| 12:33 |
kai |
bioperl, I've got an embl file like: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+12AEb1cSe2x+[libs_EQ_{embl_SP_emblcon}-AccNumber:GG657757]+-e |
| 12:34 |
kai |
and I'd like to reconstruct the sequence from the join() statement in there |
| 12:40 |
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| 12:43 |
kai |
but given that this embl file doesn't have a sequence, I can't seem to get it to even load in Bio::SeqIO |
| 12:44 |
kai |
at least $seq_obj->next_seq seems to return undef |
| 12:54 |
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| 13:10 |
dbolser |
ahhhh.... |
| 13:11 |
dbolser |
pyr will know |
| 14:06 |
kai |
ah, part pebkac |
| 14:08 |
dbolser |
ing? |
| 14:08 |
dbolser |
I was messing with this somewhere near Bio::SeqLocateable and Seq::Split |
| 14:08 |
dbolser |
its too easy to forget how the objects fit totgether |
| 14:43 |
kai |
got it.. wasn't that hard after all, I typoed the -file parameter and didn't get an error |
| 14:58 |
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| 14:59 |
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| 16:50 |
CIA-57 |
bioperl-live: Chris Fields master * r58e9c33 / t/Annotation/Annotation.t : add simple test for number of nodes returned - http://bit.ly/9vmVUM |
| 16:54 |
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| 16:54 |
deafferret |
dbolser: bioperl != real_life ? ;) |
| 17:01 |
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| 17:28 |
CIA-57 |
bioperl-live: Chris Fields master * rdd7a316 / (17 files in 6 dirs): Merge branch 'topic/gjuggler_tree_fixes' - http://bit.ly/duDmsq |
| 17:46 |
dbolser |
kai: heh |
| 17:47 |
dbolser |
deafferret: of course not ;-) |
| 17:47 |
dbolser |
its all 'computers' |
| 17:47 |
dbolser |
;-) |
| 18:03 |
CIA-57 |
bioperl-live: Jason Stajich topic/tree_dbsqlite_memoryfix * r6a7d3d2 / Bio/DB/Tree/Store/DBI/SQLite.pm : change order for columns (+21 more commits...) - http://bit.ly/9ZrM6Y |
| 18:12 |
CIA-57 |
bioperl-live: Jason Stajich topic/tree_dbsqlite_memoryfix * rb4aa255 / Bio/DB/Tree/Node.pm : test remove comment here - http://bit.ly/agjNgI |
| 18:12 |
CIA-57 |
bioperl-live: Jason Stajich master * re56f436 / (Bio/DB/Tree/Node.pm Bio/DB/Tree/Store/DBI/SQLite.pm): Merge branch 'topic/tree_dbsqlite_memoryfix' of github.com:bioperl/bioperl-live (+6 more commits...) - http://bit.ly/dfB1EY |
| 18:14 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rbee00ae / Bio/TreeIO/TreeEventBuilder.pm : Small documentation fix. - http://bit.ly/96Kau1 |
| 18:14 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * ra95434f / Bio/DB/Tree/Node.pm : Merge branch 'topic/tree_dbsqlite_memoryfix' of github.com:bioperl/bioperl-live into topic/tree_dbsqlite_memoryfix - http://bit.ly/c8ODYA |
| 18:22 |
CIA-57 |
bioperl-live: Chris Fields master * r5376d73 / (Bio/DB/Tree/Node.pm Bio/DB/Tree/Store/DBI/SQLite.pm): |
| 18:22 |
CIA-57 |
bioperl-live: Revert "Merge branch 'topic/tree_dbsqlite_memoryfix' of github.com:bioperl/bioperl-live" |
| 18:22 |
CIA-57 |
bioperl-live: This reverts commit e56f436d16cddcc1660c046e4d67d05122ecce9f, reversing |
| 18:22 |
CIA-57 |
bioperl-live: changes made to 579a85cbc2bf5ae301eef0e27aab77b7823c09dd. - http://bit.ly/9HAVnI |
| 19:45 |
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| 20:09 |
CIA-57 |
bioperl-live: Jason Stajich topic/tree_dbsqlite_memoryfix * rd10cc30 / Bio/SearchIO/blast.pm : moved some of the documentation to main POD - http://bit.ly/aikyB7 |
| 20:15 |
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| 20:15 |
CIA-57 |
bioperl-live: Jason Stajich topic/tree_dbsqlite_memoryfix * r1ed2b0a / Bio/DB/Tree/Store/DBI/SQLite.pm : test commit - http://bit.ly/bB43TQ |
| 20:25 |
CIA-57 |
bioperl-live: Chris Fields master * r7dcf3d1 / t/Annotation/Annotation.t : |
| 20:25 |
CIA-57 |
bioperl-live: fixes to deal with changes in sort order of nodes due to Bio::Tree |
| 20:25 |
CIA-57 |
bioperl-live: changes - http://bit.ly/aH898v |
| 20:25 |
CIA-57 |
bioperl-live: Chris Fields master * r7626e18 / Bio/TreeIO/newick.pm : rm $Id - http://bit.ly/cPzt0C |
| 20:43 |
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| 20:48 |
CIA-57 |
bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r81bf58d / Bio/DB/Tree/Node.pm : some more functions rolled in - http://bit.ly/dve0ZS |
| 20:48 |
CIA-57 |
bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r41c113b / Bio/DB/Tree/Store/DBI/SQLite.pm : some helper function - http://bit.ly/bG1QxJ |
| 20:51 |
CIA-57 |
bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r1ae693e / t/Tree/Node.t : no more $ - http://bit.ly/coWtMs |
| 20:56 |
CIA-57 |
bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * ra08e429 / t/Tree/DB/NodeDB.t : test for NodeDB -- minimal - http://bit.ly/c9xnIP |
| 20:56 |
CIA-57 |
bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r9f04269 / Bio/DB/Tree/Node.pm : Node methods for node_id - http://bit.ly/cO8Zas |
| 21:33 |
CIA-57 |
bioperl-live: Hilmar Lapp master * r505c4b4 / Bio/Event/EventHandlerI.pm : Added developer and method documentation. - http://bit.ly/9BhKRR |
| 21:37 |
|
deejoe_ is now known as deejoe |
| 21:58 |
CIA-57 |
bioperl-live: Hilmar Lapp master * rb7e5b79 / .shipit : This file was a mistake, Chris says. - http://bit.ly/cCY6QI |
| 21:59 |
CIA-57 |
bioperl-live: Hilmar Lapp master * r169c1bb / Bio/TreeIO/NewickParser.pm : |
| 21:59 |
CIA-57 |
bioperl-live: Made it a BioPerl object (inherit from Bio::Root::Root) and change die() to |
| 21:59 |
CIA-57 |
bioperl-live: throw(). - http://bit.ly/dtudMh |
| 22:19 |
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| 23:09 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rc229090 / Bio/Event/EventHandlerI.pm : Added developer and method documentation. - http://bit.ly/aw67lK |
| 23:09 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * re67c9a6 / Bio/TreeIO/TreeEventBuilder.pm : Documentation fixes. - http://bit.ly/aIzGAF |
| 23:09 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rb6613bc / Bio/DB/Tree/Store.pm : Adding the interface for the DBI:: module(s). - http://bit.ly/bvmvdh |
| 23:09 |
CIA-57 |
bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r0967229 / (4 files in 2 dirs): |
| 23:09 |
CIA-57 |
bioperl-live: As there may be more than one event handler for the tree parsers, changing the |
| 23:09 |
CIA-57 |
bioperl-live: name of the current one to what it actually does (creating objects). |
| 23:09 |
CIA-57 |
bioperl-live: Initializing a second one that will create database transactions instead. - |
| 23:09 |
CIA-57 |
bioperl-live: http://bit.ly/buAOJ4 |
