Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-23

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:01 carandraug joined #bioperl
01:03 Jun joined #bioperl
02:21 CIA-95 bioperl-live: Jonathan "Duke" Leto topic/cjfields_interpro_get_dbxref * r42712cb / t/Ontology/IO/interpro.t : Add some tests for get_members and protein_count and refactor tests for get_dbxrefs - http://bit.ly/94tZox
02:21 CIA-95 bioperl-live: Jonathan "Duke" Leto topic/cjfields_interpro_get_dbxref * r5b72ea0 / t/Ontology/IO/interpro.t : Add tests for class_list, get_examples and get_external_documents - http://bit.ly/bnL1zG
02:21 CIA-95 bioperl-live: Jonathan "Duke" Leto topic/cjfields_interpro_get_dbxref * r2a7e75f / t/Ontology/IO/interpro.t : Add a test for get_references and to_string - http://bit.ly/dsAV1q
02:21 CIA-95 bioperl-live: Chris Fields topic/cjfields_interpro_get_dbxref * r70501ac / Bio/Ontology/InterProTerm.pm : more fixes for warnings; tests are passing - http://bit.ly/cDk2J2
05:07 faceface joined #bioperl
06:04 bag_ joined #bioperl
06:41 bag_ joined #bioperl
08:29 faceface deafferret: nope, never used it
09:23 dmb_ joined #bioperl
10:04 flu_ joined #bioperl
10:04 spekki0 joined #bioperl
10:17 flu joined #bioperl
10:17 spekki0 joined #bioperl
12:47 ank joined #bioperl
12:52 brandi joined #bioperl
12:52 brandi left #bioperl
12:53 brandi1 joined #bioperl
12:53 brandi1 left #bioperl
13:05 glinda joined #bioperl
13:06 glinda Hi, I'm a bioperl newbie so I'm not even sure if my question is best answered by bioperl. I have a list of refseqs (NC_XXX) and I wish to downloaf for each refseq: 1. the fasta file of the sequence 2) the gff file for the annotations.
13:52 Jun I am not sure about the second question. But for the first one, you may consider to use Bio::DB::EUtilities
15:12 pyrimidine rbuels: finally got around to testing fangly's commits
15:13 pyrimidine he mangled the tests, will have to fix them for a release
15:19 deafferret roll back, make his fix them?
15:19 deafferret n/win 40
15:26 CIA-95 bioperl-live: Chris Fields master * raee9fe2 / (6 files in 2 dirs): move Bio::Assembly::IO tests into their own directory for consistency; we're not following the 10/20/30 system for tests - http://bit.ly/b079Vk
15:28 dbolser 10/20/30?
15:28 dbolser who owns CIA-95 ?
15:31 deafferret don't see it mentioned in the wiki   :(
15:34 CIA-95 bioperl-live: Chris Fields master * ra30498a / (t/Assembly/IO/bowtie.t t/Assembly/IO/sam.t t/Assembly/core.t): cleanup tests, passing but file cleanup not in place yet - http://bit.ly/c37gVB
15:34 pyrimidine CIA-95 is a CIA.vc bot for github
15:36 pyrimidine if you have a CIA.vc account, you can work on the bot
15:36 pyrimidine http://cia.vc/account/bots/17973/
15:36 pyrimidine could be smarter, just haven't had the tuits to work on it
15:38 deafferret added to wiki. thanks
15:38 pyrimidine beat me to it :)
15:39 pyrimidine just updated the main page to point to the actual IRC wiki page as well
15:39 pyrimidine deafferret: feel free to play with the bot, let me know if you run into issues with CIA.vc
15:41 deafferret thanks, but my distraction queueue already runneth over  :)
15:41 deafferret ququeueuuequueuuqeuqueueuueeuueuee
15:51 dbolser you two should choose nicks with different lengths
15:51 * dbolser decrees
15:51 dbolser I was going to ask if you could get the bot to report wiki updates
15:52 dbolser ty
15:52 dbolser NOW STAY DOWN!
15:52 de[tab] well volunteered!
15:52 dbolser wah?
15:52 * dbolser hies
15:52 dbolser hides
15:52 dbolser what was the last bot I volunteerd?
15:52 dbolser I forgot?
15:53 dbolser I think it was git hub commits?!
15:54 dbolser //topic http://bioperl.org/wiki/IRC#Getting_help |  http://www.bioperl.org/wiki/Using_Git | paste to http://perl.pastebin.com/
15:54 dbolser //topic http://bioperl.org/wiki/IRC#Getting_help |  http://www.bioperl.org/wiki/Using_Git | paste to http://bioperl.pastebin.com/
16:24 dbolser where should I put files that I want to test? in bioperl-live that is
16:25 de[tab] t/data ?
16:25 dbolser ty de[tab]
16:25 dbolser you told me that once
16:25 de[tab] damn... now OUR lengths are the same
16:25 dbolser DOH!¬
16:26 dbolser wait... when I'm the one talking I don't care
16:26 dbolser (color is different)
16:26 dbolser but my brain just distinguishes 'others' by length of nick ;-)
16:26 dbolser like the way all people of the same height look identical tome
16:27 dbolser de[tab]: do I need to document those files anywhere?
16:28 de[tab] um... not really? searching the t/ should show which file(s) use those file(s), and the .t files should explain why / what they're testing
16:28 dbolser rtfsc
16:28 dbolser de[tab]: I feel like I've nutered you
16:28 * de[tab] hopes ot
16:29 de[tab] n
16:29 * de[tab] checks
16:29 driley_ joined #bioperl
16:29 de[tab] nope, all good
16:29 dbolser you look 7/10ths of the man you where
16:30 dbolser were
16:30 brandi joined #bioperl
16:30 brandi left #bioperl
16:32 jhamilton_ joined #bioperl
16:32 dbolser hello jhamilton_
16:33 dbolser I saw david douches talk at Wag
16:35 dnewkirk joined #bioperl
16:38 dbolser so agp format referrs to a piece of dna as an 'object'
16:38 dbolser http://www.ncbi.nlm.nih.gov/projects/gen​ome/assembly/agp/AGP_Specification.shtml
16:38 dbolser I figure I shouldn't pass that nomenclature on to our fragile users
16:39 dbolser This can be a chromosome, scaffold or contig.
16:39 * dbolser goes with 'assembly'
16:49 * pyrimidine worried about dbolser talking to himself
16:50 pyrimidine they have medication for that
16:50 pyrimidine :)
17:09 CIA-95 bioperl-live: Chris Fields master * ra7be379 / t/Assembly/IO/sam.t : clean up generated index files - http://bit.ly/c9vlAZ
17:10 de[tab] theres medication for being ignored? sign me up!  :)
17:16 CIA-95 bioperl-live: Chris Fields master * r8a8d142 / t/RemoteDB/SwissProt.t : test count off on skip (ID mapper appears to be having some issues) - http://bit.ly/b0u3eg
17:19 CIA-95 bioperl-live: Chris Fields master * r4249053 / t/RemoteDB/GenPept.t : remote db ID change causing fail - http://bit.ly/cKLFnu
17:19 pyrimidine rbuels: tests should all pass again, and the assembly files should be cleaned up
17:21 pyrimidine afk # out to lunch, in more ways than one
17:22 * dbolser wonders where the strange voices are coming from
17:22 dbolser rewriting my AGP parser for Assembly/IO is harder than I thought it would be
17:22 * dbolser goes home
17:30 pyrimidine dbolser: if it's too hard, maybe think of contributing it as a script
17:30 pyrimidine or a Bio::Tools::* (generic parser)
17:31 pyrimidine really afk # for reals this time.
17:51 dbolser this is pretty cool: http://www.youtube.com/watch?v=​ioKBB5y3z5k&feature=related
17:55 dbolser pyrimidine: the problem is this... all the assembly IO formats implement the assembly as contigs nested within scaffolds, with seqLocateable within contigs
17:55 dbolser agp is somewhat different
17:55 dbolser so I'm trying to follow what those parsers do, but adapt it to what I have done...
17:56 dbolser should I cram in a single seqLocateable for each contig? and how to handle multiple 'assemblies'?
18:13 dbolser so is id a synonym for seq_id in a SeqFeature::Generic or a SeqFeature::Annotated?
18:14 dbolser SeqFeature::Generic vs. SeqFeature::Annotated, compare and contrast. 25 marks, 5% of this term.
18:19 de[tab] youtube link:  wow
18:42 dbolser de[tab]: saul is uber
18:42 dbolser night
18:47 jhamilton joined #bioperl
18:51 de[tab] g/night
18:51 pyrimidine SF::Annotated is deprecated (at least in my mind)
19:44 CIA-95 bioperl-live: Chris Fields master * r605c9dd / (4 files in 3 dirs): Merge branch 'topic/cjfields_interpro_get_dbxref' - http://bit.ly/9ejsR8
19:44 CIA-95 bioperl-live: Chris Fields master * rda9d584 / (MANIFEST MANIFEST.SKIP maintenance/symlink_script.pl): [RT 54702] patch symlink_script.pl, thanks to Curtis Jewell, and update MANIFEST/MANIFEST.SKIP - http://bit.ly/cooF4M
19:56 lulinha joined #bioperl
19:56 lulinha left #bioperl
19:59 brandi joined #bioperl
20:02 CIA-95 bioperl-run: Chris Fields master * rd586822 / (2 files in 2 dirs): [RT 58464] patching to allow file names with spaces - http://bit.ly/duLe1g
20:02 CIA-95 bioperl-run: Chris Fields master * r4024088 / (3 files): add dots param - http://bit.ly/9UoXaN
20:02 CIA-95 bioperl-run: Chris Fields master * r0205676 / (3 files):
20:02 CIA-95 bioperl-run: Revert "add dots param"
20:02 CIA-95 bioperl-run: This reverts commit 4b82f66543326d8afd13cd4a585e9552eca2ab5b. - http://bit.ly/bdh7yA
20:05 CIA-95 bioperl-live: Chris Fields master * r2bfc2c9 / Bio/Tools/Run/WrapperBase.pm : [RT 58464] patching to allow file names with spaces - http://bit.ly/bQ1a5B
20:05 brandi left #bioperl
20:15 CIA-95 bioperl-db: Chris Fields master * r98d2a0f / (3 files): [RT 44466] remove corba-related scripts, now obsolete - http://bit.ly/doTrcv
21:01 jhamilton joined #bioperl
21:01 pyrimidine left #bioperl
22:04 bag_ joined #bioperl
23:04 spekki0 joined #bioperl
23:15 driley joined #bioperl
23:30 genehack` joined #bioperl

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary