Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-09

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All times shown according to UTC.

Time Nick Message
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04:56 pyrimidine burp.... good hackathon.....
04:56 pyrimidine :P
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05:57 deafferret /win 45
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09:11 dbolser who's hacking?
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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
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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/c​gi-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
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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
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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
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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
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16:54 deafferret dbolser: bioperl != real_life   ?    ;)
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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
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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
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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
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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
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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

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