Time |
Nick |
Message |
00:08 |
|
ank left #bioperl |
00:10 |
|
ank joined #bioperl |
01:56 |
|
Drin_ joined #bioperl |
01:59 |
|
Drin left #bioperl |
02:18 |
|
scottcain joined #bioperl |
03:04 |
|
scottcain left #bioperl |
03:14 |
|
scottcain joined #bioperl |
03:55 |
|
Drin_ left #bioperl |
04:14 |
|
scottcain left #bioperl |
10:03 |
|
svaksha left #bioperl |
12:29 |
|
svaksha joined #bioperl |
12:42 |
dbolser |
can I use a DAS adaptor for a SF:Store in the same way as a mysql adaptor? |
13:15 |
dbolser |
rbuels: about you're AGP BP module... |
13:15 |
|
scottcain joined #bioperl |
13:15 |
dbolser |
how much work is it for it to inherit SeqFeature::StoreI? |
13:16 |
dbolser |
It would be painfully useful for me right now if I could use an AGP object as a GBrowse adaptor |
13:16 |
dbolser |
hello scottcain |
13:16 |
scottcain |
good morning dbolser |
13:38 |
|
pyrimidine left #bioperl |
14:08 |
|
pyrimidine joined #bioperl |
14:24 |
|
scottcain left #bioperl |
14:43 |
CIA-119 |
bioperl-run: Chris Fields master * r5d1d9d4 / Changes : a few last additions - http://bit.ly/fZ6j6e |
15:31 |
rbuels |
dbolser: that AGP object shouldn't be a SeqFeature::StoreI. but something could either inherit from or encapsulate *it* and glue it to SeqFeature::StoreI |
15:32 |
|
svaksha left #bioperl |
15:33 |
|
svaksha joined #bioperl |
15:34 |
|
scottcain joined #bioperl |
15:41 |
CIA-119 |
bioperl-run: Chris Fields master * raec2981 / Build.PL : passthrough Makefile is deprecated; add BEDTools dependency - http://bit.ly/fEDO36 |
15:41 |
CIA-119 |
bioperl-run: Chris Fields master * rfa29acb / (3 files in 2 dirs): hack in a workaround for version(), which conflicts with the -version parameter for BLAST+ - http://bit.ly/fOUGMF |
15:50 |
CIA-119 |
bioperl-run: Chris Fields master * rfe5e5c0 / t/BEDTools.t : skip # off - http://bit.ly/hn9qjh |
15:51 |
|
scottcain left #bioperl |
15:55 |
dbolser |
rbuels: why is that better? |
15:55 |
dbolser |
(me knows nothing) |
15:56 |
dbolser |
rbuels: also, can you define a standard AGP -> GFF conversion and a) implement it in the AGP stuff you're doing and b) document it on the SO 'GFF best practice' page? |
15:56 |
rbuels |
dbolser: so that people don't need all of bioperl to parse an AGP. |
15:56 |
dbolser |
rbuels: right |
15:56 |
dbolser |
that makes sense! |
15:57 |
rbuels |
unless, like you, they want it. |
15:57 |
dbolser |
sure |
15:57 |
rbuels |
dbolser: you seen it in sheenams github? |
15:57 |
rbuels |
dbolser: her pre-project was extracting that. |
15:57 |
rbuels |
dbolser: https://github.com/sheenams/Bio-AGP |
15:58 |
rbuels |
dbolser: it's almost ready to go to cpan |
15:58 |
rbuels |
dbolser: that's gonna be her next task. |
16:01 |
dbolser |
rbuels: awesome! |
16:02 |
rbuels |
dbolser: feel free to submit pull requests. it would be good for her to learn how they work. |
16:02 |
dbolser |
ok |
16:02 |
* dbolser |
begins stalking sheenams on github |
16:02 |
rbuels |
(she's got a proposal in to get started on the bioperl breakup for gsoc) |
16:03 |
rbuels |
(and it's a good proposal) |
16:03 |
dbolser |
yeah, I caught some of that discussion in here |
16:03 |
dbolser |
your master plan is coming together! |
16:03 |
rbuels |
yep |
16:03 |
dbolser |
slash and... slash |
16:03 |
rbuels |
everything takes so *long* though |
16:03 |
* rbuels |
sighs |
16:04 |
dbolser |
rbuels: so long as each unit of functionality reduces the time taken to the next |
16:05 |
rbuels |
dbolser: you talk to any PIs in your neighborhood about github for genomes? |
16:05 |
rbuels |
really, somebody just needs to write a big grant and get money and do it |
16:09 |
dbolser |
rbuels: ... |
16:09 |
dbolser |
could that somebody be me? |
16:09 |
rbuels |
could be. |
16:09 |
dbolser |
I need a job that overlaps with my hobby |
16:09 |
rbuels |
need more people though too |
16:09 |
dbolser |
more than the current 70% |
16:09 |
rbuels |
people with big powdered wigs |
16:09 |
dbolser |
yeah... |
16:10 |
rbuels |
to hem and haw and say how *interested* they are |
16:10 |
dbolser |
I'm just of the opinion whatever I do EBI will poop on |
16:10 |
rbuels |
maybe you need to work with EBI then |
16:10 |
dbolser |
and unfortunately, I can't go to ebi |
16:10 |
dbolser |
heh |
16:15 |
* pyrimidine |
just got an image of Triumph the Insult Comic Dog |
16:16 |
rbuels |
dbolser: you don't have to go to ebi, just find somebody in there that's interested in doing this |
16:17 |
rbuels |
dbolser: and do a collaboration |
16:17 |
rbuels |
or something. |
16:20 |
dbolser |
rbuels: ic |
16:20 |
dbolser |
just a quick question... If AGP object 'contains' several AGP components, how do you call the reverse relationship? |
16:21 |
dbolser |
An AGP component 'belongs to' an AGP object? |
16:21 |
|
scottcain joined #bioperl |
16:21 |
dbolser |
'is part of'? |
16:21 |
rbuels |
is a component of? |
16:21 |
rbuels |
something like that |
16:21 |
dbolser |
ok |
17:31 |
CIA-119 |
bioperl-network: Chris Fields master * r9b0a1b5 / t/IO_psi10.t : get tests passing - http://bit.ly/dLThzi |
17:31 |
pyrimidine |
:) |
17:34 |
CIA-119 |
bioperl-network: Chris Fields master * r3cae3e6 / Build.PL : passthrough Makefile deprecated - http://bit.ly/h2MC66 |
17:35 |
CIA-119 |
bioperl-network: Chris Fields master * ra69d973 / Changes : small Changes update - http://bit.ly/gc5xsD |
17:43 |
CIA-119 |
bioperl-network: Chris Fields master * r6caa4eb / Build.PL : add stub module_name - http://bit.ly/eYBp64 |
19:37 |
pyrimidine |
rbuels: around? |
20:01 |
|
sullen joined #bioperl |
21:07 |
|
barbae_inpexae joined #bioperl |
21:19 |
|
sullen left #bioperl |
21:30 |
|
scottcain left #bioperl |
21:35 |
|
scottcain joined #bioperl |