Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-12-21

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All times shown according to UTC.

Time Nick Message
00:58 bioperl-bot joined #bioperl
01:00 bioperl-bot joined #bioperl
01:05 bioperlbot joined #bioperl
01:06 brunov joined #bioperl
01:06 brunov bioperlbot, help
01:06 bioperlbot brunov: Ask me for help about: message, join, karma, auth, seen, seqtools, infobot, loader, rss, title (say 'help <modulename>').
01:06 brunov cpan++
01:06 brunov bioperlbot, karma cpan
01:06 bioperlbot brunov: cpan has karma of 1.
01:06 brunov cpan++
01:07 brunov karma cpan
01:07 bioperlbot cpan has karma of 2.
01:07 brunov bioperlbot++
01:07 bioperlbot brunov: Thanks!
01:07 brunov bioperlbot, help seqtools
01:07 bioperlbot brunov: Various tools for DNA sequences: translation, reverse complement, composition, etc. Must address me directly.
01:07 bioperlbot ..Usage:
01:07 bioperlbot ..
01:07 bioperlbot ..    translate   <seq> [FRAME] # Translates DNA to protein
01:07 bioperlbot ..    composition <seq>         # Base pair composition
01:07 bioperlbot ..    revcomp     <seq>         # Reverse complement
01:07 bioperlbot ..    reverse     <seq>         # Reverse
01:07 bioperlbot ..    complement  <seq>         # Base pair complement
01:07 bioperlbot ..    tm          <seq>         # Calculate the melting temperature
01:07 bioperlbot ..    mw          <seq>         # Compute the molecular weight
01:07 brunov bioperlbot, leave #bioperl
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02:44 brunov bioperlbot, leave
02:44 bioperlbot left #bioperl
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02:58 driveby_bot /home/svn-repositories/bioperl: r16547 (maj) : bug squish
02:59 driveby_bot joined #bioperl
02:59 driveby_bot /home/svn-repositories/bioperl: r16548 (maj) : test fixes
03:21 driveby_bot joined #bioperl
03:21 driveby_bot /home/svn-repositories/bioperl: r16549 (maj) : test fixes
06:01 driveby_bot joined #bioperl
06:01 driveby_bot /home/svn-repositories/bioperl: r16550 (kortsch) : Added guesser for bowtie alignment output format and fixed unreasonable tightness on first field of crossbow guesser - also placed entries in alphabetical order.
07:47 bioperl-bot joined #bioperl
07:47 brunov bioperl-bot, /join #biobot-test
07:47 brunov bioperl-bot, join #biobot-test
07:47 bioperl-bot brunov: Ok.
07:49 brunov bioperl-bot, tell rbuels that you should try me!
07:49 bioperl-bot brunov: OK. I'll deliver the message.
08:38 bag joined #bioperl
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11:55 driveby_bot /home/svn-repositories/bioperl: r16551 (dave_messina) : moved writing of closing </seqXML> tag from DESTROY to close().
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13:20 brunov bioperl-bot, hi?
13:20 brunov bioperl-bot, help
13:20 bioperl-bot brunov: Ask me for help about: biodigest, message, join, karma, auth, seen, retort, seqtools, infobot, loader, rss, title (say 'help <modulename>').
14:25 brandi1 joined #bioperl
14:37 brunov someone around
14:37 brunov ?
14:37 brunov :/
14:42 bioperl-bot left #bioperl
14:48 bioperl-bot joined #bioperl
14:49 brunov bioperl-bot, join #biobot-test
14:49 bioperl-bot brunov: Ok.
14:51 faceface_ joined #bioperl
16:31 faceface hey brunov
16:31 brunov hey
16:31 faceface I like the idea of RSS watching by bioperl-bot
16:32 brunov faceface, cool, just feel free to add feeds
16:32 brunov bioperl-bot, help RSS
16:32 bioperl-bot brunov: rss [add uri|remove|list]
16:32 faceface cool
16:32 brunov :)
16:32 faceface did it get vetoed from bioinformatics?
16:32 brunov no, they just asked me to have it not spit the titles of url links
16:33 brunov and it wasn't very welcomed, so there was no point in it being there
16:33 faceface rss add http://seqanswers.com/forums/exter​nal.php?type=RSS2&amp;forumids=10
16:33 bioperl-bot [ SEQanswers - Literature Watch ]
16:33 faceface brunov: I'd like it to be there.
16:33 faceface ~bioinformatics ++
16:33 brunov well, but they won't allow feeds there
16:33 faceface #bioinformatics ++
16:34 faceface meh, orbitz can be a jerk
16:34 brunov #bioinformatics--
16:34 brunov bioperl-bot, orbitz?
16:34 bioperl-bot brunov: orbitz is a douche
16:43 brunov well, I just found out that RSS is channel specific
16:44 brunov bioperl-bot, rss add http://seqanswers.com/forums/exter​nal.php?type=RSS2&amp;forumids=10
16:44 bioperl-bot brunov: [ SEQanswers - Literature Watch ]
16:44 bioperl-bot brunov: Ok.
16:44 brunov bioperl-bot, rss list
16:44 bioperl-bot brunov: http://seqanswers.com/forums/exter​nal.php?type=RSS2&amp;forumids=10
16:46 faceface cool
16:46 faceface although, that is more of a bioinformatics feed than a bioperl feed
16:46 brunov faceface, I just made it join #bioinfo
16:47 brunov you can play with it
16:47 brunov the Title plugin (the one that speaks url links) is unloaded
16:47 faceface tyty
16:47 faceface okok
16:48 faceface Although I liked that too
16:49 brunov yeah, sucks that some people don't know about /ignore
16:49 brunov although I understand that if it gets too annoying you have to do something about it
16:49 brunov although I'd wait for it to become annoying before bitching
16:49 faceface brunov: I've asked people in
16:49 faceface brunov: I've asked people in
16:49 faceface brunov: I've asked people in #bioinformatics to 'try it and see'
16:49 brunov faceface, oh, cool
16:50 brunov faceface, you can also make them join #biobot-test, so that you don't bother people at #bioinfo
16:50 brunov if they want to abuse the bot, make them go there instead i guess
17:00 * deafferret feeds the phant
17:00 faceface oh dear
17:00 faceface brunov: watch this...
17:00 brunov ok
17:01 faceface bioperl-bot: rss add http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot faceface: Ok.
17:01 bioperl-bot RSS: Li Ruotti 2009 <http://seqanswers.com/w/index.php?title=Li​_Ruotti_2009&amp;diff=1293&amp;oldid=prev>
17:01 bioperl-bot RSS: RSEM/URL 0 <http://seqanswers.com/w/index.php?title=​RSEM/URL_0&amp;diff=1292&amp;oldid=prev>
17:01 bioperl-bot RSS: RSEM <http://seqanswers.com/w/index.php?tit​le=RSEM&amp;diff=1291&amp;oldid=prev>
17:01 bioperl-bot RSS: CnD/URL 0 <http://seqanswers.com/w/index.php?title​=CnD/URL_0&amp;diff=1290&amp;oldid=prev>
17:01 bioperl-bot RSS: Simpson 2009 <http://seqanswers.com/w/index.php?title=S​impson_2009&amp;diff=1289&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: CnD <http://seqanswers.com/w/index.php?ti​tle=CnD&amp;diff=1288&amp;oldid=prev>
17:01 bioperl-bot RSS: IGV <http://seqanswers.com/w/index.php?ti​tle=IGV&amp;diff=1287&amp;oldid=prev>
17:01 bioperl-bot RSS: IGV/URL 0 <http://seqanswers.com/w/index.php?title​=IGV/URL_0&amp;diff=1286&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: IGV <http://seqanswers.com/w/index.php?ti​tle=IGV&amp;diff=1285&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: MAQGene <http://seqanswers.com/w/index.php?titl​e=MAQGene&amp;diff=1283&amp;oldid=prev>
17:01 bioperl-bot RSS: BFAST <http://seqanswers.com/w/index.php?tit​le=BFAST&amp;diff=1282&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: SOAPsnp <http://seqanswers.com/w/index.php?titl​e=SOAPsnp&amp;diff=1281&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: SOAPsnp/URL 0 <http://seqanswers.com/w/index.php?title=S​OAPsnp/URL_0&amp;diff=1280&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: SOAPsnp <http://seqanswers.com/w/index.php?titl​e=SOAPsnp&amp;diff=1279&amp;oldid=prev>
17:01 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:01 bioperl-bot RSS: 19420381 <http://seqanswers.com/w/index.php?title​=19420381&amp;diff=1277&amp;oldid=prev>
17:01 bioperl-bot RSS: Crossbow/URL 0 <http://seqanswers.com/w/index.php?title=Cr​ossbow/URL_0&amp;diff=1276&amp;oldid=prev>
17:01 bioperl-bot RSS: 19930550 <http://seqanswers.com/w/index.php?title​=19930550&amp;diff=1275&amp;oldid=prev>
17:01 bioperl-bot RSS: Crossbow <http://seqanswers.com/w/index.php?title​=Crossbow&amp;diff=1274&amp;oldid=prev>
17:01 deafferret um... laugh
17:01 bioperl-bot RSS: GATK <http://seqanswers.com/w/index.php?tit​le=GATK&amp;diff=1273&amp;oldid=prev>
17:01 bioperl-bot RSS: EagleView <http://seqanswers.com/w/index.php?title​=EagleView&amp;diff=1272&amp;oldid=prev>
17:02 bioperl-bot RSS: 19880367 <http://seqanswers.com/w/index.php?title​=19880367&amp;diff=1271&amp;oldid=prev>
17:02 bioperl-bot RSS: SAMtools <http://seqanswers.com/w/index.php?title​=SAMtools&amp;diff=1270&amp;oldid=prev>
17:02 bioperl-bot RSS: MAQ <http://seqanswers.com/w/index.php?ti​tle=MAQ&amp;diff=1269&amp;oldid=prev>
17:02 deafferret *plonk*
17:02 bioperl-bot RSS: MapNext <http://seqanswers.com/w/index.php?titl​e=MapNext&amp;diff=1268&amp;oldid=prev>
17:02 brunov bioperl-bot, leave #bioperl
17:02 bioperl-bot left #bioperl
17:02 brunov phew
17:02 brunov faceface, sorry
17:02 brunov I guess it wasn't a good idea after all
17:02 brunov deafferret, hey! you are back! I wrote a bot!
17:02 deafferret sweet! too bad I ignored it already  :)
17:03 faceface I have kind of killed any hope of getting it in bioinformatics now ;-)
17:04 deafferret fix it, I'm sure it could be useful
17:04 bioperl-bot joined #bioperl
17:04 brunov deafferret, done
17:04 brunov sorry
17:04 brunov faceface, yeah, not a big loss anyway
17:04 deafferret no worries  :)
17:05 brunov bioperl-bot, be deaferret?
17:05 * bioperl-bot feeds the phant
17:07 faceface brunov: fixed already?
17:07 brunov yeah
17:07 faceface ...
17:07 faceface bioperl-bot: rss add http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:07 * faceface tremmors
17:07 brunov :)
17:09 * faceface waits...
17:09 brunov faceface, I unloaded the RSS plugin, I guess it wasn't a good idea after all :/
17:10 brunov do you guys think it would be useful? I went by the wiki page saying that it'd be a nice thing to have
17:10 brunov it does some dna/protein stuff so far
17:11 brunov and I uploaded those plugins to github, so you can hack on them or add your own
17:11 brunov bioperl-bot, cure cancer
17:11 brunov that's a TODO
17:11 deafferret brunov: -sigh-  bioperl-bot just killed all the humans  :(
17:12 brunov oh noes
17:12 faceface oh
17:13 faceface bioperl-bot: rss remove http://seqanswers.com/w/index.php?tit​le=Special:RecentChanges&amp;feed=rss
17:13 faceface oh ... heheh
17:13 faceface never mind
18:57 driveby_bot joined #bioperl
18:57 driveby_bot /home/svn-repositories/bioperl: r16552 (maj) : bug squish
18:58 driveby_bot joined #bioperl
18:58 driveby_bot /home/svn-repositories/bioperl: r16553 (maj) : DOH!
19:04 driveby_bot joined #bioperl
19:04 driveby_bot /home/svn-repositories/bioperl: r16554 (maj) : better checking
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19:23 * deafferret needs a hard definition of miRNA seed site
19:23 deafferret one that's programmatically applicable
19:23 * deafferret wishes $self luck
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20:56 driveby_bot /home/svn-repositories/bioperl: r16555 (cjfields) : fix test count
20:57 deafferret rock on... cluster job has run EMBOSS merger 50M times and counting...
20:57 deafferret been running for 5 weeks so far
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21:09 driveby_bot /home/svn-repositories/bioperl: r16556 (cjfields) : pull seqfeatures by name, check primary tags against original sfs prior to revcom, then check that the location is actually revcom correctly
21:18 deafferret whoah... sudden meltdown  http://www.targetscan.org/cgi-bin/targetscan/ver​t_50/targetscan.cgi?species=Human&amp;gid=&amp;m​ir_sc=&amp;mir_c=&amp;mir_nc=&amp;mirg=miR-513a
21:18 bioperl-bot [ Targetscan 5.1: predicted miRNA targets ]
21:20 deafferret what the... uh. somebody kick that server please  :)
23:02 ptl how do you kick a server? using DDoS?
23:03 deafferret :)
23:03 deafferret WinNuke
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23:45 driveby_bot /home/svn-repositories/bioperl: r16557 (maj) : consistent directories

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