Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2014-06-11

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All times shown according to UTC.

Time Nick Message
05:26 byte48 joined #bioperl
09:35 carandraug joined #bioperl
11:56 mnb joined #bioperl
12:34 scottcain joined #bioperl
15:24 scottcain Hi all, a few months ago, I think I was here with a problem with Bio::DB::SeqFeature::Store and how it interacted with Bio::DB::IndexedBase causing GFF loading to fail when there either was or was not fasta at the end of the file (I don’t remember which).  Does anybody remember if that was fixed?
15:24 scottcain I feel like it was, but now I can’t find any evidence of it.
15:41 Dustin_ joined #bioperl
15:41 Dustin_ Hey guys. Anyone here?
15:52 trs scottcain: it was when a GFF didn't have sequence data.
15:53 trs scottcain: either in an external sidecar fasta or embedded.
15:53 scottcain That’s what I kind of thought
15:53 trs scottcain: I don't think it was fixed per se since a SeqFeature, reasonably, wants to sequence to associate the feature with.
15:54 trs I do have the irc logs from then
15:54 scottcain trs: except that it’s not: features are about coordinates on a sequence, but you don’t necessarily need residues to go with them.
15:55 Dustin_ There's people! May I have a moment of someone's time to ask a (probably stupid) question?
15:56 scottcain Dustin_: you can ask.  Probablilty of me knowing the answer is low :-)
15:57 trs scottcain: sure, here was how our discussion on 23 April ended. :)  http://tsibley.net/paste/201​4-06-11GbwFPguB-bioperl-gff
15:58 Dustin_ Awesome. When downloading/installing bioperl through fink I use the command fink install bioperl-pm5162, just as a preface. In any case, that ran for a good amount of time until I received the following error: Failed: Problem resolving dependencies. Check for circular dependencies. So then I tried restarting the install.
15:58 trs Dustin_: always Just Ask and then idle in the channel for a day or so.  Otherwise people can't answer you asynchronously.
15:58 scottcain trs: thanks for that—I was thinking that discussion was via email for a while and it was driving me crazy that I couldn’t find it.
15:58 trs Dustin_: see also the channel topic.
15:58 trs scottcain: I have the whole discussion if you want it.
15:58 scottcain trs: nope that’s good enough
15:59 * trs & for a bit
16:00 Dustin_ https://gist.github.com/ano​nymous/91535312b0b265162c15
16:00 Dustin_ That's the output
16:00 * scottcain hates fink and installing on Macs in general, even though I’ve been using them for years.
16:01 Dustin_ Heh. I just recently joined a lab as an undergrad and she figured out I know C++ and Java and threw me on the computer on perl and I'm entirely clueless
17:38 looper joined #bioperl
17:39 trs Dustin_: I wouldn't use fink.

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