Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-10

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All times shown according to UTC.

Time Nick Message
00:03 driveby_bot joined #bioperl
00:03 driveby_bot /home/svn-repositories/bioperl: r16970 (cjfields) : Razi's patch for parsing out the algorithm reference, gets tests working again
00:03 driveby_bot Diff: http://tinyurl.com/2b5cwjv
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14:21 deafferret hmm... so how do I catch warnings with this Bio::Root::Exception gizmo?
14:23 deafferret $@ isn't getting set like the wiki says
14:24 deafferret while (eval { $seq = $in->next_seq } ) {
14:30 deafferret oh... i got it
14:55 deafferret bummer... Carp got rid of shortmess and longmess  ?
15:27 spekki01 .
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16:58 Jun joined #bioperl
17:02 abooz I'm still having problems when trying to parse a gff3 file. I've managed to make comply with the standards, so it passes the online validator, but i still get a parent not ound message.
17:03 abooz I've uploaded the code and error message here: http://codepad.org/sxfvq3GE but it's just copy and paste of a basic example from the documentation.
17:04 jhannah looking
17:05 abooz i should paste the sample file somewhere.
17:05 jhannah is 13101.t00002 in the file?
17:06 abooz yes.
17:06 jhannah hm. so you understand the error and the relevant data looks good?
17:06 jhannah apparently your gff asserts a relationship that bioperl fails to parse
17:08 abooz http://codepad.org/jMrSHi4O here is the data but i'm afraid the paste edited the tabs to spaces.
17:08 abooz yeah, but i don't see why. THe online validator @ wormbase finds it normal.
17:15 jhannah tabs--
17:16 abooz Individually each feature can be read correctly.
17:16 abooz It's the paste.
17:17 jhannah ### means "the rest of this file is comments"   ?
17:18 abooz what?
17:18 jhannah i'm guessing
17:18 jhannah what does ### do?
17:20 abooz This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until
17:24 abooz but you are right.Without ### everything works find and i'm an idiot.
17:24 abooz Thanks!
17:25 jhannah really?
17:25 jhannah hmm... ya
17:25 jhannah ignorance wins again!  :)
17:27 abooz that's the part that fooled me: It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
17:27 jhannah i don't understand why ### is bad for the 2nd line after ###   assuming what you pasted is indeed what ### does
17:27 rbuels jhannah: ### is a sync mark for parent relationships
17:28 jhannah but but but
17:28 rbuels jhannah: so your parser doesn't have to keep the whole file in memory in order to deal with any subfeatures that might come later in the file
17:29 Jun Hi, abooz. Besides the gff "###", you may have an error in your code.
17:29 jhannah rbuels:  http://github.com/jhannah/​sandbox/tree/master/abooz/
17:29 Jun you can not write something like (push @array, @array)
17:29 jhannah run gffparser.pl
17:30 * jhannah sees no other errors
17:30 Jun Ok, maybe I am wrong :D
17:31 jhannah Jun: pretty sure that push is fine... ?
17:31 jhannah I don't use parens there but I don't think that hurts anything
17:32 jhannah looks like a bioperl bug in relation to ### ... somewhere
17:33 abooz it also throws errors in relation with metadata.
17:33 abooz but i can live with that.
17:33 jhannah ESTACKFULL
17:34 jhannah abooz: do you NEED ### or were you just being fancy?
17:34 jhannah (I have zero real-world gff projects)
17:35 abooz This is not my file. It's rice annotation.
17:35 jhannah bah! who eats rice?  ;)
17:35 abooz :D
17:35 pyrimidine joined #bioperl
17:36 jhannah uh ph
17:36 jhannah we have awakened the pyrimidine
17:37 pyrimidine first time in a few weeks I've had time to join
17:37 Jun Moring boss!
17:37 jhannah bug of the minute:   http://github.com/jhannah/​sandbox/tree/master/abooz/  gffparser.pl
17:37 Jun Finally see u in the channel :D
17:37 pyrimidine I was on a couple of times over the last few weeks, just not enough
17:38 pyrimidine $job
17:38 pyrimidine abooz: Bio::FeatureIO in bioperl is an abomination.  It needs to be taken out back and shot.
17:39 pyrimidine (as well as Bio::SeqFeature::Annotation)
17:39 abooz :)
17:39 pyrimidine great idea, bad implementation
17:39 * pyrimidine not feeling like pulling punches today
17:40 Jun BTW, I just ordered "Higher Order Perl" from Amazon today. Hopefully it will arrive this week.
17:41 Jun It should be good ...
17:41 pyrimidine I'm currently working on cleaning up and refactoring that code, but it's taking backseat to other obligations ATM
17:41 pyrimidine Jun: good!  it's a great book for ideas
17:41 Jun And, I think I can actually start to work this week. Hopefully it will be a good start.
17:42 Jun I was quite occupied too for the last two weeks ... I need to write two manuscripts on microarray analysis ...
17:42 jhannah abooz: ha! looks like a too-late-by-one error in Bio/FeatureIO/gff.pm
17:43 pyrimidine jhannah: that wouldn't surprise me
17:43 Jun Just finished a draft manuscript today. and, the other manuscript is on the way. So I finally get my hands free...
17:43 jhannah lol... yuip
17:44 jhannah abooz: add another BS entry below ### and suddenly the relationship works fine
17:44 abooz lol
17:44 jhannah the line below ### is getting grouped above the ###
17:44 jhannah after that it's fine
17:44 jhannah cause the flag is set too late
17:44 jhannah ... so close! have a cookie
17:45 pyrimidine that's a nasty bug
17:45 jhannah pyrimidine: worth patching?
17:45 jhannah or are you going to shoot it anyway  ;)
17:46 pyrimidine worth patching on trunk, maybe writing up some tests for (they can be merged to a refactor)
17:46 jhannah but doing thing the Right Way is so much work!  :o)
17:47 pyrimidine just tests then, maybe TODO
17:47 jhannah git commit -m "trust me, this is totally fixing shit"
17:47 pyrimidine :P
17:47 jhannah lol    I'll patch it unless abooz is going to
17:47 jhannah on Thr after d-day
17:48 abooz test, the right way?What are all these things? Where are we?
17:51 * pyrimidine working on cleaning up main trunk bugs...
17:52 pyrimidine jhannah: have you run tests on main trunk with perl 5.12 yet?
17:53 jhannah ya, in smolder
17:53 Jun Just a question. Is there an easy way to install the modules in the lastest trunk?
17:53 jhannah http://biobase2.ist.unomaha.edu:8​080/app/projects/smoke_reports/1  top report
17:53 jhannah Jun: Build.PL ?
17:54 Jun Last time when I found the modules, the codes are in html page...
17:54 jhannah Jun: hmm? git clone the github.com bioperl-test repo, then run Build.PL
17:55 pyrimidine I don't think you want to install modules from latest trunk.  Place them in PERL5LIB locally, or set up a local repo.
17:56 pyrimidine It's generally not a good practice to install code that is considered in development, unless you don't necessarily care about the possible bugs present
17:56 Jun ok, place them locally should be better
17:58 jhannah abooz: are you patching this one or am I?
17:59 abooz feel free. I don't have much experience with stuff like that. Don't want to break things.
17:59 pyrimidine nothing to break that isn't already broken
17:59 jhannah :)   k, i'll break...err fix it then  :)
17:59 jhannah emails himself a post-github rollout reminder
18:03 pyrimidine github migration will be this wed.
18:03 pyrimidine then you can go fork yourself
18:04 jhannah mmmmm...
18:07 jhannah Tony: "I serve the American people at the pleasure of ... myself. And one thing you can always count on me to do is pleasure myself."
18:07 jhannah Iron Man 2
18:07 jhannah & # airport
18:16 driveby_bot joined #bioperl
18:16 driveby_bot /home/svn-repositories/bioperl: r16971 (cjfields) : missing test file
18:16 driveby_bot Diff: http://tinyurl.com/2wrd3hz
18:20 driveby_bot joined #bioperl
18:20 driveby_bot /home/svn-repositories/bioperl: r16972 (cjfields) : make test less prone to volatile changes
18:20 driveby_bot Diff: http://tinyurl.com/23vlnze
18:34 driveby_bot joined #bioperl
18:34 driveby_bot /home/svn-repositories/bioperl: r16973 (cjfields) : use settable n, fall back to num_hsps (more consistent with recent changes)
18:34 driveby_bot Diff: http://tinyurl.com/2dbcyoh
18:37 driveby_bot joined #bioperl
18:37 driveby_bot /home/svn-repositories/bioperl: r16974 (cjfields) : HSP n defaults to 1 (must have at least one HSP used for score/e-val/p-val)
18:37 driveby_bot Diff: http://tinyurl.com/253m4sg
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18:55 driveby_bot /home/svn-repositories/bioperl: r16975 (cjfields) : remote database update, local dump file needed to be updated to match remote database change
18:55 driveby_bot Diff: http://tinyurl.com/27h8l2n
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19:00 driveby_bot /home/svn-repositories/bioperl: r16976 (cjfields) : load Bio::DB::Fasta (this fails with SQLite tests)
19:00 driveby_bot Diff: http://tinyurl.com/2dmtoac
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19:04 driveby_bot /home/svn-repositories/bioperl: r16977 (cjfields) : remote change in ensembl, make a little less prone to future changes
19:04 driveby_bot Diff: http://tinyurl.com/2g9prlc
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19:09 driveby_bot /home/svn-repositories/bioperl: r16978 (cjfields) : 1170 -> 1770 (matches data)
19:09 driveby_bot Diff: http://tinyurl.com/2fq8zrg
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20:05 driveby_bot /home/svn-repositories/bioperl: r16979 (cjfields) : commenting out a section of code fixes test crashes from improperly munged data.  Needs the author to take a look, but it seems the related code wasn't doing anything but somehow changing data in-place
20:05 driveby_bot Diff: http://tinyurl.com/2e2vyux
20:09 jhannah pyrimidine++ # look at him go! he's unstoppable!
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20:16 pyrimidine down to two failing tests now
20:20 jhannah CAN YOU SMELL WHAT THE pyrimidine IS COOKIN'!?!?!
20:20 * jhannah roars pro-wrestler style
20:20 Jun potato???
20:20 Jun smashed potato with spring onion ...
20:21 jhannah live video feed of pyrimidine : http://www.youtube.com/watch?v=Mr8glaM4ruM
20:22 jhannah http://www.youtube.com/watch?v=​9PoGqGusvQo&feature=related
20:31 jhannah ok, rat genome, you're going down
20:31 jhannah prepare to be boarded
20:31 pyrimidine that sounded ...bad
20:31 jhannah oh?
20:31 pyrimidine boarding a rat?
20:32 jhannah the Great Ship of State that is the latest rat assembly
20:32 jhannah aka "my bitch"
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20:46 driveby_bot /home/svn-repositories/bioperl: r16980 (cjfields) : rework assembly tests to be more modular, should make it easier to add more as needed, turn others off, etc
20:46 driveby_bot Diff: http://tinyurl.com/349t78k
20:46 pyrimidine down to one failing
20:48 jhannah pyrimidine++ # provisional
21:00 Jun are you guys still there?
21:01 jhannah yup
21:01 Jun I am thinking of reorganizing Bio::SimpleAlign methods into different categories
21:02 Jun It may be good to categorize them into "known category", for example, accoring to some commonly used alignment softwares
21:02 Jun so that the new package can be accepted faster...
21:03 Jun so what is the software you will use to view/edit alignment files?
21:03 Jun besides clustalx...
21:03 Jun and seaview ...
21:03 Jun any other recommended tools?
21:03 pyrimidine jalview would prob be the most common one I can think of
21:03 Jun yep, you are right
21:04 Jun actually it goes with Clustalw in the EBI server...
21:05 Jun I will have a look at Jalview. It may be a good reference :D
21:05 pyrimidine I think that's a good start.  Just think about which methods would work better as a separate set of util subs and which work better integrated into the class
21:06 Jun ok, i will work on that
21:06 pyrimidine I actually have to head out.  I will be back on tomorrow (I have a meeting to get to, then home)
21:07 pyrimidine but feel free to email me.  Saw your post to the list, and I'll try to respond tonight.
21:07 Jun I think generally, I will divide the methods into "internal attribute related" and "outer visiting funcion"
21:08 Jun The post was supposed to answer a guy's question. It is ok.
21:08 pyrimidine okay
21:08 Jun ok, see u then. Hopefully, I can give you a report on the new structure of the Bio::SimpleAlign this week.
21:09 Jun We will see ~~
21:09 pyrimidine You probably already have a checkout, but after Wed that should be easier via github.  You can either fork off the bioperl repo then or we can make a branch for the ALign work
21:09 pyrimidine okay, see ya
21:09 spekki01 when using eutilities - esearch, i specify the -db => 'nucleotide' where can i check what databases this db encompases, such as Genbank, REFSEQ, etc...?
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