Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-01-25

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All times shown according to UTC.

Time Nick Message
00:37 driveby_bot joined #bioperl
00:37 driveby_bot /home/svn-repositories/bioperl: r16745 (kortsch) : Quick results file option
03:13 driveby_bot joined #bioperl
03:13 driveby_bot /home/svn-repositories/bioperl: r16746 (kortsch) : Quick results option can now create objects
03:37 driveby_bot joined #bioperl
03:37 driveby_bot /home/svn-repositories/bioperl: r16747 (cjfields) : silence error if $id is undef
03:43 driveby_bot joined #bioperl
03:43 driveby_bot /home/svn-repositories/bioperl: r16748 (cjfields) : [bug 2836] add namespace to command line args, other bits (courtesy Dan Bolser)
03:52 driveby_bot joined #bioperl
03:52 driveby_bot /home/svn-repositories/bioperl: r16749 (cjfields) : remove leftover debugging fluff
03:54 driveby_bot joined #bioperl
03:54 driveby_bot /home/svn-repositories/bioperl: r16750 (cjfields) : deal with som eodd strand issues popping up
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05:04 driveby_bot joined #bioperl
05:04 driveby_bot /home/svn-repositories/bioperl: r16751 (cjfields) : [bug 2901] Deal with div by zero in cases where gaps exist (per Janet Young).  In cases where this occurs, using 'NA' as a placeholder.  Passes all tests, but this may be changed to something else if warranted.
05:08 driveby_bot joined #bioperl
05:08 driveby_bot /home/svn-repositories/bioperl: r16752 (cjfields) : some docs for that last commit (tests to come)
05:19 driveby_bot joined #bioperl
05:19 driveby_bot /home/svn-repositories/bioperl: r16753 (cjfields) : tests for bug 2901
05:22 driveby_bot joined #bioperl
05:22 driveby_bot /home/svn-repositories/bioperl: r16754 (kortsch) : Paired end tests - Now *BETA*
05:28 driveby_bot joined #bioperl
05:28 driveby_bot /home/svn-repositories/bioperl: r16755 (cjfields) : prettier output
13:16 driveby_bot joined #bioperl
13:16 driveby_bot /home/svn-repositories/bioperl: r16756 (maj) : transcribe and rev_transcribe
13:16 driveby_bot joined #bioperl
13:16 driveby_bot /home/svn-repositories/bioperl: r16757 (maj) : tests for transcribe and rev_transcribe
13:31 driveby_bot joined #bioperl
13:31 driveby_bot /home/svn-repositories/bioperl: r16758 (cjfields) : change NA to -1
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15:37 nachocab Hi, how can I partition a RichSeq object that contains a whole genome into all its genes
15:41 nachocab anyone?
15:45 perl_splut joined #bioperl
16:01 driveby_bot joined #bioperl
16:01 driveby_bot /home/svn-repositories/bioperl: r16759 (maj) : check for is_pseudo on executable/executables call
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16:13 driveby_bot /home/svn-repositories/bioperl: r16760 (maj) : last change was redundant, this better
18:21 deafferret nachocab: still around?
18:24 driveby_bot joined #bioperl
18:24 driveby_bot /home/svn-repositories/bioperl: r16761 (maj) : remove a cygwin kludge
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19:36 perl_splut at least the bot is appropriately named
19:38 deafferret ?
19:38 perl_splut driveby_bot
19:38 perl_splut it comes, it spams with changes and it runs off
19:38 deafferret yes, many the day it terrorizes this neighborhood
19:39 perl_splut I like that it shows the commit comment
19:39 perl_splut works well as long as the commits are kept atomic
19:40 * rbuels counts the number of people writing bioinformatics code that know what that means
19:41 deafferret "usefully atomic"  ?
19:41 deafferret :)
19:41 deafferret commit message 1: "almost done"
19:41 rbuels lol
19:41 deafferret commit message 2: "pretty close"
19:41 deafferret commit message 3: "done"
19:41 deafferret commit message 4: "oops"
19:41 rbuels here's one of my favorites: "bleh"
19:41 deafferret my boss has the worst commit messages EVA
19:42 deafferret "devel" or "lots of stuff"
19:42 perl_splut yeah, that would get a ban... :)
19:42 deafferret :)   "but perl_splut told me to! in *IRC*!!"
19:42 deafferret HR might not be amused
19:42 perl_splut I said the commits should be atomic... not the message
19:43 deafferret well, if the commits are usefully atomic then a corresponding, useful message should come with
19:43 deafferret git++ # cleaner commits
20:00 deafferret unless people's eyeballs can filter dirty SVN branch commits...
20:00 * deafferret thinks "atomic commit" is poorly named since in its own definition it talks about splitting the atom, ruining the analogy...
20:02 space_agent1 left #bioperl
20:02 deafferret these 15 subobjects are bundled into one "atomic commit," the atom being an indivisible object ... what?
20:04 rbuels lol
20:05 deafferret phant: is he laughing at me or with me?
20:06 deafferret .o@  ...   .
20:06 deafferret phant: not very helpful   :(
20:06 rbuels hehe
20:20 deafferret arguably, every SVN commit is atomic (if you try to commit 15 files and the 5th fails, none are committed), hence my "usefully atomic" nomenclature to talk about "is your single commit complete and useful as a set of features / corrections to the project"
20:21 * rbuels needs to write a phant bot that does nothing but abuse deafferret
20:21 rbuels well, it would also poop 2 or 3 times a day
20:21 * deafferret thought that was what "rbuels" was
20:21 rbuels lol
20:33 deafferret current phant-cam poop camera triggers after any extended deafferret AFK
20:33 deafferret (motion-sensor)
21:34 nachocab deafferret: I'm back :)
21:34 deafferret nachocab: welcome back  :)
21:35 nachocab so I'm wondering if I'm going about it the right way: I want to get the sequence of all the genes of a bacterium
21:35 nachocab so I downloaded the genome in genbank format
21:35 nachocab and now I did $genome->get_SeqFeatures();
21:36 nachocab and then @cds_features = grep { $_->primary_tag eq 'CDS' && $_->has_tag('gene') } @features;
21:36 nachocab but some genes are missing
21:36 deafferret "missing" ?
21:36 nachocab I get less entries in @cds_features than what it says in NCBI
21:37 nachocab is the right way to do it? grep { $_->primary_tag eq 'CDS' && $_->has_tag('gene') }
21:38 deafferret I think that should work. Can you isolate one you're definately missing?
21:38 nachocab I haven't looked into it too much yet, I was just looking for guidance
21:38 nachocab I thought there would be an easier way to get all the genes of a genome
21:39 deafferret http://gist.github.com/286277 <-- I wrote that on Friday and it worked fine
21:39 nachocab that's great, thanks!
21:39 deafferret isolate one that it skipped that you expected it not to skip. stick that in a file. share it with us so we can help
21:40 nachocab I'm a complete perl newbie, so code like that helps a lot
21:40 deafferret you fooled me, you seem to have a better grasp than most  :)
21:41 nachocab I know Ruby, and I tried BioRuby, but BioPerl just seems much better documented
21:41 * deafferret laughs
21:41 deafferret \o/
21:41 deafferret there's lots of good wiki walk-throughs. tutorials and HOWTOs and such
21:42 nachocab yeah, I'd also like to follow the mail group, but the interface seems really clunky. I wonder why they don't use google groups...
21:42 deafferret most people subscribe, so the emails come to their inbox
21:43 deafferret if you're a gmail addict, just subscribe to the list with your gmail account
21:43 nachocab all right, I will
21:43 nachocab thanks for your help Jay
21:43 deafferret sure. there were 4 of us in here earlier
21:49 deafferret nachocab: did you find one that's definately missing?
21:49 deafferret you're not getting 0 results, are you?
21:53 deafferret man... jobs that take 2.5 days to run are really frustrating... My brain is not geared for this work
21:53 deafferret maybe if I was drunk...
21:54 nachocab jajaj
21:54 nachocab no, I'm getting 2265 instead of 2425
21:55 nachocab but it's allright, I'll figure it out
21:55 deafferret otay. if you get stuck tell us the gene you're expecting to have that you don't, and the genome accession number, and we can run through the perl debugger for you
21:56 nachocab now that's something I'd like to see, is there something better than doing perl -debug -e 1 to go into interactive mode?
21:56 nachocab I miss the ruby console
21:56 nachocab or the R console
21:58 natetg joined #bioperl
21:58 natetg my $target=1; my $blastfactory = new Bio::Tools::Run::RemoteBlast ('-prog' => $prog, '-data'      => $db, '-expect'    => $expect, 'readmethod' => $method, 'max_target_seqs' =>$target);
21:59 natetg im having some problems getting the max target seqs to work
21:59 deafferret nachocab: nope, that's about it
21:59 natetg the default parameters are 100
21:59 natetg i want to change them to 1000 or 10000
22:01 natetg i know i have it set at 1 currently because i want to be able to test it
22:04 deafferret rbuels: going to YAPC::NA?
22:05 deafferret natetg: so what makes you think it's not working?
22:05 rbuels deafferret: yep, plan to
22:05 rbuels deafferret: i still volunteer to organize one of the dinners too
22:05 rbuels deafferret: don't think i forgot  ;-)
22:06 rbuels deafferret: if somebody just orders me "find us a place for X people to have dinner on date Y", i'll do it
22:06 deafferret rbuels: I forgot about you forgetting
22:06 deafferret apparently I'm the auctioneer this year
22:06 rbuels lol
22:06 deafferret rbuels: find us a place for 2 people to have dinner on date *
22:06 * deafferret blinks his eyelashes
22:07 deafferret err... bats. ya, that's it
22:08 rbuels lol
22:08 natetg deafferret: because when i test it there are compilation errors
22:08 deafferret natetg: http://codepad.org/ <-- paste your errors
22:08 deafferret please
22:08 deafferret :)
22:09 natetg done
22:10 deafferret natetg: URL?  :)
22:10 deafferret wow. R is 12.3GB virt mem...   (Quantile Regression)++
22:10 natetg deafferret: http://codepad.org/FWSizEUQ
22:11 deafferret natetg: cpan Bio::Tools::Run::RemoteBlast
22:11 deafferret or however you prefer installing that
22:11 deafferret um...
22:11 natetg ive installed it
22:11 * deafferret should not be helping "install" BioPerl since he... doesn't
22:11 natetg it works fine with default
22:12 deafferret use Bio::Tools::Run::RemoteBlast;   # at the top ?
22:12 natetg yea
22:12 natetg want me to paste entire code?
22:12 deafferret what does perl -MBio::Tools::Run::RemoteBlast\ 100   say?
22:14 natetg what about the "use"?
22:15 deafferret type this on a command prompt and tell me what it says:     perl -MBio::Tools::Run::RemoteBlast\ 100
22:17 natetg nothing
22:17 natetg happened
22:18 deafferret use codepad to show that to me
22:19 deafferret for example, this is what I get:   http://codepad.org/LfXMKFGx
22:21 natetg http://codepad.org/cZzAomaX
22:22 deafferret perl -M
22:22 natetg yea
22:22 natetg i saw that
22:22 deafferret right-o. try again.  :)
22:22 natetg i got same as you
22:23 natetg http://codepad.org/EwpgOGWj
22:23 deafferret oh, good. that means it is in your path. So if you 'use Bio::Tools::Run::RemoteBlast' at the top, you shouldn't get the error you showed me. so paste all your code
22:24 natetg http://codepad.org/R5Oq9MrZ
22:28 deafferret natetg: try - characters in front of your args
22:29 natetg deafferret: what does that do?
22:30 deafferret dunno. maybe nothing. try it.
22:30 deafferret for some reason I don't grok, that's the BioPerl standard
22:34 rbuels historical reasons.
22:35 rbuels ;-)
22:36 deafferret yes, all my bugs and ugly are actually features. for historical reasons.
22:36 natetg it doesnt seem to like it
22:36 natetg thanks though for all the help
22:36 deafferret you see, I used to suck. even more than I do now.
22:36 natetg i got to get back to other work now
22:36 deafferret natetg: you'll have to be more specific. "doesn't seem to like it" doesn't help us help you
23:08 deafferret sigh ... it's hard to add tests to verify a job that take 3+ hours to run  :)

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