Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-04

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All times shown according to UTC.

Time Nick Message
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10:28 Jun Hi, anyone here? I got a problem using git. I dont know how to solve it.
10:29 Jun I deleted a file in my local repo. So when I use "git pull", it will say "error: Your local changes to 'Bio/AlignIO/pfam.pm' would be overwritten by merge
10:29 Jun .  Aborting.
10:29 Jun Please, commit your changes or stash them before you can merge.
10:31 Jun Ok, no bother. Problem solved ... It seems I have to say "git add ." in the top directory. Then everything will be added
10:54 kblin ah
10:54 kblin yeah
11:13 kblin but I'm not sure if that's what you want all the time
11:13 kblin it's usually better to explicitly add the files you changed
11:14 kblin or if you removed a file, "git rm path/to/file" tells git the file is now gone
11:15 kblin git status gives you a pretty good view at what's going on in your current branch
12:23 Jun ok, i see
12:24 kblin and I can also recommend git add --interactice
12:25 kblin er --interactive
12:27 Jun Ok, I will write that down. Cheers
12:28 kblin my pleasure :)
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14:13 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | paste to http://pastebin.com/
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16:36 spekki0 hey pyrimidine, thanks for the help with that script yesterday and the tips on what to change.
16:36 pyrimidine np
16:36 pyrimidine not sure what was happening withthe 'no docsums' error, but it was sporadic
16:37 pyrimidine so, likely on NCBI's end
16:37 spekki0 i know what you mean, it seems to go away though when you remove that keep_histories option
16:37 spekki0 well at least it does for now lol
16:38 pyrimidine I saw it both with and without that set, actually
16:38 spekki0 oh really :(
16:38 spekki0 hmmm well hopefully that changing the verbose and eval blocking it will catch it, I'm working on that atm
16:38 genehack how hard would it be to modify the code to have it sleep and retry the same fetch when it gets that response?
16:39 genehack opps, great minds.
16:39 pyrimidine genehack: I'm wondering if that may be too 'top-level'
16:42 pyrimidine these were originally meant to be sort of a middle-layer for accessing eutils and other remote databases w/o the bioperl object overhead
16:42 pyrimidine (only thing I believe they are reliant on is Bio::Root::Root/IO, that's it)
16:43 pyrimidine so they could be completely separate from bioperl altogether at some point
16:45 pyrimidine I love perl 6: http://perlbuzz.com/2010/0​8/diving-into-perl-6.html
16:45 genehack pyrimidine: i was meaning to do that in the calling script, not in the library
16:45 pyrimidine genehack: ah, ok
16:45 pyrimidine yes, agree  completely
16:45 spekki0 i do have a quick question though im googling around trying to figure out how to change the verbose level, i've never done that before in perl so im not sure how to change it. Pyrimidine do you have an example of how to do that?
16:46 genehack because i suspect what's happening is you're hitting a machine in their cloud that (for whatever reason) doesn't have the same history state as the others, and that's where the bogus response comes from. re-polling will probably fix it, most of the time.
16:46 pyrimidine spekki0: just pass in '-verbose => 1' to any bioperl constructor
16:47 pyrimidine ex: my $eutil = Bio::DB::EUtilities->new(-eutil => 'einfo', -verbose => 1);
16:47 spekki0 oh well that's much easier than i figured it would be lol
16:47 spekki0 thanks
16:48 pyrimidine you'll get debugging output, BTW
16:48 pyrimidine I suppose you could just redirect that as needed to a log file or /dev/null
16:49 spekki0 k
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17:17 spekki0 how does $docsum->get_Items_by_name('GenomicInfoType'); work? is it return an object or somethign else?
17:19 genehack from the code it looks like it returns a list of objects
17:20 genehack see http://kobesearch.cpan.org/htdocs/BioP​erl/Bio/Tools/EUtilities/Summary/ItemC​ontainerI.pm.html#get_Items_by_name-
17:20 spekki0 tx
17:22 genehack random idea: a blog post showing how to use re.pl with bioperl to address issues like this would probably be really useful -- might be easier for the casual programmers to approach being able to interactively introspect what their code is doing.
17:22 genehack rbuels , pyrimidine : do random ideas like that go into bugzilla or is that just for Real Bugs?
17:23 * rbuels thinks that should not go into bugzilla
17:23 * pyrimidine agrees with rbuels
17:23 * rbuels loves gratuitous third person
17:23 kblin evening folks
17:23 * bobdole loves it too
17:24 * pyrimidine agrees with bobdole
17:24 pyrimidine which is the first time :)
17:24 rbuels lol
17:25 pyrimidine spekki0: what genehack said (array of objects)
17:26 pyrimidine spekki0, genehack: and before it's stated, I know the docs need to be addressed
17:27 genehack rbuels: okay, not in bugzilla. i'll throw it on my list of "crap to blog about" but if anybody beats me to it, i'm not gonna be all sad or anything.
17:27 spekki0 no worries, maybe pose a google summer of code project to have somone work on howto docs on stuff :)
17:28 genehack pyrimidine: i wasn't even thinking about the docs; was thinking more about alternate ways of letting people discover what is actually going on.
17:28 * deafferret prepares the disappear the enlightened
17:29 kblin GSoC projects can't be documentation only projects, unfortunately
17:30 deafferret Summer of Docs
17:32 genehack clearly we need a project to write code to generate docs.
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17:41 kblin :)
17:41 kblin automatic documentation (and manual corrections)
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18:07 * deafferret wishes rbuels would call his new mobile phone so he could enjoy the rbuels-specific "loco with the cake" ringtone
18:07 rbuels wow.
18:07 rbuels that is intense.
18:07 deafferret i swear I won't actually answer it
18:07 deafferret that would be too awkward
18:10 rbuels deafferret: ok i used up one of the 9.7 remaining units on my burner telling google voice to ring you
18:10 rbuels deafferret: who knows if that will work
18:11 deafferret um. it rang for 0.5 seconds, stopped, does not tell me i missed a call or anythign
18:11 rbuels deafferret: yes that is expected, because i hung up.
18:12 rbuels deafferret: you think these minutes grow on frickin trees?
18:12 deafferret um, shouldn't it tell me I missed a call at least?
18:12 deafferret stupid HTC Evo 4G
18:12 deafferret with android 2.2 (freshly installed this morning)
18:12 rbuels deafferret: here, you dropped something
18:12 * rbuels hands deafferret the name of his phone
18:13 deafferret corn?
18:13 rbuels don't get me started.
18:13 * deafferret adds extra rbuels-screening
18:13 deafferret ahh.... "infinite loop w/ annoying hold music"
18:14 deafferret "reconnect to random inbound telemarketing firm"
18:31 * genehack ponders why rbuels has a burner.
18:39 deafferret bunsen?
18:40 kblin dvd
18:42 deafferret aren't most dvd players also burners nowadays? paid $40 for my external USB one I think
18:42 deafferret a year ago
18:56 kblin I guess so
19:10 * pyrimidine loves my blu-ray burner, doesn't love the price of blu-ray discs
19:13 * pyrimidine has also ordered Effective Perl and the Catalyst book, thus sending $$ mst's and bdf's way
19:13 pyrimidine least it's not my $$ :)
19:14 kblin don't do blu-ray
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19:16 Lynx_ Hi all! I have a question: How can I get Bio::Index::Blast to save the index to a file?
19:18 pyrimidine kblin: agreed, not worth it
19:19 pyrimidine Lynx_: my $index = Bio::Index::Blast->new(-filename => $indexfile, -write_flag =>1);
19:19 pyrimidine -filename is the index file
19:20 Lynx_ Duh, thanks.
19:20 Lynx_ -write_flag confused me
19:20 deafferret pyrimidine: the Apress book, right?
19:20 deafferret blu-ray++
19:21 pyrimidine deafferret: re: Catalyst, yes, the Apress one
19:22 deafferret yes, good
19:22 rbuels heh
19:23 pyrimidine only one review on the Catalyst 5.8 one (and someone mentioned the relative unknown-ness of the author and his deficiency of code :)
19:23 pyrimidine not to say his book is bad, but ...
19:23 deafferret oh, the 2nd packt book is out?
19:23 pyrimidine yes
19:24 pyrimidine http://www.amazon.com/Catalyst-5-8-Perl-MVC​-Framework/dp/1847199240/ref=sr_1_cc_3?ie=U​TF8&qid=1280949680&sr=1-3-catcorr
19:24 deafferret huh. wonder if he fixed the jillions of errata from the first
19:24 pyrimidine note the author change with that one
19:24 pyrimidine not jrockway
19:25 deafferret yup. that author has shown up in #catalyst a few times
19:25 deafferret to general "good luck fixing that huge mess"
19:25 deafferret don't know how much he did or didn't fix
19:25 pyrimidine well, he got a book out of it, so not bad
19:26 pyrimidine whether anyone buys it is another story
19:27 deafferret uh, packt apparently doesn't know an excellent vs. horrendous book (the editors where the CAUSE of most errors in the 1st packt book)
19:27 deafferret were
19:28 deafferret nm. i have no first hand knowledge, so I'll shut up now
19:28 deafferret i was 70% happy with the deployment chapter of the apress book 2 weeks ago
19:29 deafferret that's the only chapter i've actively attempted to use, of any cat book
19:29 pyrimidine looks like the author of the Packt one is likely on #catalyst (solar_ant), so  won't stir the pot there
19:29 deafferret :)
19:29 pyrimidine might be using Catalyst myself locally a bit
19:29 deafferret there's several hours of discussion in my backlogs
19:30 spekki0 esummary can retreive a summary record for a accession number right?
19:30 pyrimidine no
19:30 pyrimidine you need the UID
19:30 spekki0 awe :(
19:30 pyrimidine they recently f*cked that all up with efetch as well, IIRC
19:31 pyrimidine 'gilist' no longer works for accessions
19:31 pyrimidine I think the new designation is 'seqid' or somesuch, and it returns the always parsable ASN1
19:31 pyrimidine *ASN.1
19:32 kblin asn.1, that's one of these crypto protocols, right?
19:32 pyrimidine I just started using a locally indexed LiveList for most of this conversion, myself
19:33 pyrimidine kblin: http://www.ncbi.nlm.nih.gov​/Sitemap/Summary/asn1.html
19:34 kblin pyrimidine: yeah, if you can get the docs in a secret format, it looks like a crypto protocol :)
19:35 pyrimidine kblin: :)
19:35 pyrimidine not as much secret as it is a PITA
19:36 kblin that said, I almost implemented ms-asn1.dll for wine once, I got a good look at it
19:36 pyrimidine there was a push for bindings to the NCBI toolkit, not sure how far that ever progressed
19:38 kblin blast certainly exports results in it
19:42 spekki0 just looking for an opinion, what is the best way to get the new UID for a records that has been replaced with a new record. Here are my steps so far start with esummary for each beginning record. Test the Status field, if it = replaced grab the replaced by field which gives me the accession number of the new record. put that acc# into efetch pull down the genbank record parse it and get the gi out of it. Or is there a simpler way to do thi
19:42 spekki0 s?
19:44 pyrimidine Bio::DB::SeqVersion does something like this
19:46 pyrimidine my $query = Bio::DB::SeqVersion->new(-type => 'gi');
19:46 pyrimidine my $latest_gi = $query->get_recent(2);
19:46 pyrimidine spekki0: ^^^^
19:46 spekki0 cool
19:47 pyrimidine here's a question for mr. f*cking gmod rbuels
19:47 rbuels eh what
19:47 pyrimidine why recreate load_ids for loaded GFF3, via bp_sf_load?
19:48 rbuels recreate?  where?
19:48 * pyrimidine digging up an example...
19:49 pyrimidine so, I have gene models in GFF3 with simple integer IDs
19:50 pyrimidine ID=123
19:50 pyrimidine if that is dumped via bp_sf_gff3 (or using gff3_string(1)), the ID stays intact
19:51 pyrimidine if that is reloaded into a new database, a new ID is assigned
19:52 pyrimidine I think b/c the load_id != the primary_id
19:52 rbuels pyrimidine: you can load lots of gff3 files, the IDs only are supposed to be unique within a gff3 file
19:52 rbuels pyrimidine: whereas the load_id i think is supposed to be the primary key in bp::sf::store
19:52 rbuels something like that
19:52 pyrimidine right
19:53 pyrimidine but somewhere in the dump process, the load_id becomes the ID
19:53 pyrimidine (e.g. it replaces the primary_id)
19:54 rbuels pyrimidine: probably cause the dump might not be valid gff3 if it didn't make sure the IDs it dumped were unique
19:54 rbuels cause there's no unique guarantee going in
19:54 pyrimidine yes, that's what I'm thinking
19:55 pyrimidine it's not too worrying, but we have some collabs who want GFF3 from our in-house DB, so it would be nice to have consistent IDs
19:56 pyrimidine at least it doesn't push the old primary ID over to Alias (which it did a year or two ago)
19:56 rbuels ugh
19:56 pyrimidine Just wish there was a way to make the script not forcibly do this
20:00 spekki0 tx again pyrimidine that seqversion worked so well.
20:01 pyrimidine np
20:02 rbuels pyrimidine: do you have a commit bit?  i can give you one if you need it
20:02 * rbuels chuckles
20:05 pyrimidine commit bit for?
20:06 pyrimidine silly man
20:08 pyrimidine rbuels: of, course, if you gave me a commit bit for gmod, I would wreck holy havoc on the code there :)
20:09 rbuels pyrimidine: oh, it needs some holy havoc.  what's your sourceforge login?
20:12 pyrimidine mwahaha
20:13 deafferret rbuels: you haven't moved them to github? slacker!
20:13 rbuels pyrimidine: ok, you have your commit bit
20:14 * pyrimidine now plots the downfall of gmod
20:14 pyrimidine :-D
20:14 rbuels deafferret: they will move to github.  just ... need to wait a little more
20:14 rbuels actually, i'm thinking that the projects will just move piecemeal
20:15 rbuels i plan to agitate for gbrowse to move starting about a month from now
20:15 rbuels and after that i will agitate for chado
20:15 pyrimidine rbuels: that should be interesting
20:15 rbuels and that's about the only projects that are active and are not already on github
22:11 CIA-93 bioperl-live: Nathan Liles master * r2281176 / scripts/Bio-DB-GFF/genbank2gff3.PLS :
22:11 CIA-93 bioperl-live: Fixed convert_to_name() to name tag features with only ID (e.g the region
22:11 CIA-93 bioperl-live: feature) - http://bit.ly/9BIOFj
22:39 deafferret ENEEDTESTS
23:30 ank joined #bioperl
23:43 rbuels i am starting to think that nathan should not be committing to master.
23:44 rbuels well, that's only in genbank2gff3
23:50 deafferret is that patch bad? or just no tests?

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