Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-03

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All times shown according to UTC.

Time Nick Message
08:23 faceface ende, I'm aware of a few projects ...
08:24 faceface yum repos for bioinformatics ...
08:33 rbuels faceface: which are you aware of?
08:33 faceface rbuels: ones maintained at bioinformatics.org
08:33 faceface biorpm
08:33 faceface and others... I have a list somehwere
08:33 faceface also there are repos for R
08:34 faceface and bioconductor
08:34 faceface my friend pingou is working on that
08:35 faceface rbuels: what time do you call this? ;-)
08:35 rbuels erm, 1:35am for me
08:35 faceface (pingou is in #bioinformatics)
08:35 faceface well past your bedtime?
08:35 rbuels pretty much
08:36 rbuels i was just talking about bio packaging with my boss today
08:36 faceface 8-)
08:36 rbuels it's a very undermet need
08:36 faceface rbuels: I really want to integrate the efforts at bioinformatics.org
08:37 rbuels there is a lot of packaging work being done out there, but not a lot of traction being made in distribution
08:37 faceface they have the necessary resources to manage the repo, we just need ... well... we need coordination damit!
08:37 faceface yes
08:37 rbuels do they actually have the resources to maintain a bunch of packages though?
08:37 rbuels cause maintaining a package is actually no picnic
08:37 faceface (or my new favourite afforism 'Agree.')
08:37 faceface me personally?
08:38 rbuels resources = people time
08:38 faceface lets switch to #bioinformatics and try to get pingou to comment
08:38 rbuels is bioinformatics.org run in your joint?
08:38 faceface no
08:38 rbuels sure fine.
08:46 pingou joined #bioperl
08:46 pingou hi
08:49 faceface yo p
08:49 * pingou borrows a tab key to faceface
09:00 faceface pingou: but 'p' sounds 'street'
09:39 northind joined #bioperl
09:47 northind left #bioperl
15:19 deafferret faceface should share his joint(s)
15:27 deafferret back to the grind  http://github.com/jhannah/​sandbox/tree/master/erlang
15:48 alper joined #bioperl
16:07 johnraekwon joined #bioperl
16:09 johnraekwon Hi, noob here with a question about bioperl/biosql - I've noticed (or think I have noticed) that load_seqdatabase.pl does not parse the InterPro optional ID (which is the domain name/type).  At least, I don't find this entry (or its value) in the database after running the script on a test file (I am using a SwissProt .dat proteome file)... I have managed to write a little stub to view this info... and now I am trying to merge the two,
16:11 deafferret hi johnraekwon. I'm not familiar with that field. You could post your question to the bioperl-l mailing list, and/or help us patch BioPerl if it needs a patch   http://github.com/rbuels/bioperl-live/tree/master
16:12 deafferret and/or post your stub somewhere  :)
16:12 johnraekwon Hi there... just about to post to the mailing list...
16:12 johnraekwon sure, I can upload the stub... it is weak, but shows the info... where should I place it
16:12 johnraekwon this is my first time getting into this community
16:12 deafferret I like github.  :)
16:13 johnraekwon I'll have a look at that.. http: I guess?
16:13 deafferret or http://sial.org/pbot/
16:13 deafferret http://github.com/
16:13 johnraekwon http://github.com/
16:13 johnraekwon yeah got it
16:13 deafferret one time paste easier on sial.org
16:14 johnraekwon ok... its crazy how many different things are going on... of course, the numerous options are great, but a little consolidation would help too... the BioPerl wiki is pretty cool
16:14 johnraekwon anyway, I'll hit the list and throw the stub up and see what comes...
16:14 johnraekwon more soon
16:15 deafferret :)   life seems non-convergent  :)
16:15 deafferret nerd life anyway
16:15 johnraekwon Ah, but the trick is to converge where is seems a near impossibility right...
16:15 johnraekwon that is the geek sword fight
16:36 deafferret johnraekwon: sure. in-channel is fine.
16:36 deafferret this is a very sleepy channel
16:37 johnraekwon cool
16:37 johnraekwon so, I went to the website and opened an accout
16:37 johnraekwon then I am presented with a page of things I should do
16:37 deafferret do you use version control?
16:37 johnraekwon I downloaded and installed what I take to be a git 'client'
16:37 deafferret of any kind?
16:37 johnraekwon I have, but not regularly
16:38 johnraekwon I am on os X for the most part
16:38 johnraekwon I have been using svn and cpan from time to time
16:38 johnraekwon but it is real easy to break this system... and I have been burned before
16:38 deafferret SVN++.  :)   git is like that
16:38 deafferret your desktop you mean?
16:38 johnraekwon OK..
16:38 johnraekwon yeah, exact
16:38 johnraekwon so, now that I have an account
16:39 johnraekwon I need to configure the client I guess
16:39 johnraekwon with my username...
16:39 johnraekwon --global user.name
16:39 johnraekwon is this correct
16:39 deafferret what's your username?
16:39 johnraekwon johnraekown
16:39 johnraekwon i got the binary from here: http://git-scm.com/download
16:39 johnraekwon and installed
16:40 johnraekwon now I am just sitting here open jawed
16:40 deafferret hmm... github.com seems to not know who user johnraekown is
16:40 johnraekwon ugh..
16:41 johnraekwon maybe takes a minute to propagate?
16:41 deafferret It might. You should be able to run Terminal.app and then issue git commands
16:41 johnraekwon i can send you a screen shot
16:41 deafferret like   git --global user.name "John Raekwon"
16:41 johnraekwon ...actually, not sure how to do that on irc
16:41 johnraekwon ;-)
16:42 johnraekwon exactly..
16:42 deafferret IRC and git are 2 different things
16:42 johnraekwon so, I should set that global stuff
16:42 johnraekwon first
16:42 johnraekwon yeah, i realie that
16:42 johnraekwon I realize that is
16:42 johnraekwon ok one sec..
16:42 deafferret so, when you run Terminal.app and type 'git' do you see git?
16:42 johnraekwon let me locate the git program and try to enter my username etc.
16:42 johnraekwon I'll be back
16:43 johnraekwon yeah that is the thing
16:43 johnraekwon i dont see it.. but probably need to add to my PATH
16:43 johnraekwon so, better find the install directory
16:43 johnraekwon obviously not usr/bin
16:44 deafferret so you're getting    -bash: git: command not found   ?
16:46 johnraekwon exact
16:48 deafferret here  http://git-scm.com/download   you clicked to download the OS X binary (Stable)  ?
16:49 deafferret and then ran that?
16:49 johnraekwon yes
16:50 johnraekwon I did a locate on it, and get a bunch of junk... but this may be relevant: /usr/share/man/man3/Tcl_UniCharIsDigit.3tcl.gz
16:50 deafferret ls -al /usr/bin/git    ?
16:50 johnraekwon oops
16:50 johnraekwon hold on
16:50 johnraekwon no such thing
16:52 deafferret find / -name "git" 2>/dev/null
16:52 johnraekwon yeah, very strange... I got the GITGUI it says cannot find git in path
16:52 johnraekwon but it is not clear where is the path... WTF
16:53 johnraekwon strange it would just install to some mysterious location... seeing what I can find online
16:57 johnraekwon got it working
16:58 johnraekwon left #bioperl
16:58 johnraekwon joined #bioperl
16:58 johnraekwon fell off...
16:58 johnraekwon back now
16:59 johnraekwon got the git working, or rather, found where it was installed, and added to PATH
17:00 deafferret whoah... Erlang you sexy beast
17:01 johnraekwon ...what is the business about adding a public key?
17:01 deafferret so github.com has to know it should trust stuff sent from your desktop
17:01 johnraekwon OK, how can I convince it ;-)
17:01 deafferret so you need to attach your pub ssh key to your account
17:02 deafferret http://github.com/guides/providing-your-ssh-key
17:02 johnraekwon found a tutorial... reading
17:02 johnraekwon ...your quick
17:02 johnraekwon you're... uggh
17:04 johnraekwon is it important to use a passphrase?
17:05 johnraekwon I just hit enter..
17:05 deafferret i don't
17:05 johnraekwon ok.. cool. i'll continue on
17:05 deafferret yay!   http://github.com/johnraekwon
17:12 johnraekwon The authenticity of host 'github.com (65.74.177.129)' can't be established.
17:12 johnraekwon RSA key fingerprint is 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48.
17:12 johnraekwon what do you make of this...
17:16 johnraekwon OK... now I need to upload the stub I suppose...
17:18 deafferret that's normal the first time
17:19 faceface deafferret: can you help with a very basic qu
17:20 * deafferret can try
17:20 faceface got a $hit = $SearchIO->next_result->next_hit
17:20 faceface and I got the name of the hit using $hit->name
17:20 faceface but how do I get the query name?
17:21 faceface do I really need to go $hit->hsp->query->name()?
17:22 deafferret probably, ya. does that work?
17:22 * faceface is too stubborn to try
17:23 faceface where are docs for query object?
17:24 deafferret um... I usually use perl -d and then the deobfuscator
17:24 deafferret print ref $hit->hsp->query
17:24 * faceface gets very confused
17:25 faceface deafferret: I can't believe its not in hit somwhere, or at least in hsp
17:25 faceface but I can't find docs...
17:25 faceface oh wait... my exmples page
17:25 deafferret well, with the debugger you don't need docs. you just x the object  :)
17:25 faceface $hit->name(),
17:25 deafferret it's either in there or it's not
17:25 faceface its in result!
17:25 deafferret or Data::Dumper it
17:25 faceface query_name()
17:26 faceface I always forget the result itterator
17:26 faceface $result = $SearchIO->next_result; $result->query_name()
17:26 faceface awesome
17:27 faceface tiling is pretty cool
17:27 faceface I can finally ignore those pesky HSPs
17:29 johnraekwon deafferret... think I uploaded the stub
17:30 deafferret I only see one repo and it only has a README file
17:30 johnraekwon .. damn it!
17:30 johnraekwon yeah, I see that too...
17:30 johnraekwon try again..
17:37 johnraekwon ...I am choking on this... can you lend some syntax
17:37 johnraekwon I have placed my file in the repository locally
17:37 johnraekwon need to sync that with the remote
17:37 johnraekwon I tried add and commit... not working... I am not doing it correctly
17:45 johnraekwon I get the message that everything is up to date...
17:45 johnraekwon but clearly not
17:45 johnraekwon what exactly is supposed to happen when it opens vim on issuing git commit
17:46 deafferret git add; git commit; git push
17:46 deafferret you type your comment about the change in there.
17:50 johnraekwon 'right... but when I quit VIM, I get an error
17:50 johnraekwon and then push doesnt work
17:57 johnraekwon dude.. success
17:57 johnraekwon only 2 hours for the a simple task... I'm hopeless ;-)
17:58 johnraekwon So, I guess you have already the bioperl-db script load_seqdatabase.pl?
18:05 deafferret um, ya, I can grab a copy from wherever it lives
18:06 deafferret http://sial.org/pbot/  is for just pasting something trivial once
18:06 deafferret git is for global domination  :)
18:07 karbak joined #bioperl
18:08 johnraekwon i get url not found on the sial site
18:10 johnraekwon http://search.cpan.org/~cjfields/BioPerl-d​b-1.6.0/scripts/biosql/load_seqdatabase.pl
18:10 johnraekwon this is the version I am using
18:21 deafferret sorry, sucked deep into Erlang today
18:21 deafferret distracted  :)
18:22 dhoss joined #bioperl
18:22 johnraekwon no worries... any help you can offer is appreciated... we all got our main gig
18:23 deafferret this is $gig[1]->tangent   :)
18:25 * dhoss is a whore, and takes whatever gigs he can get
18:28 faceface deafferret: I'm seeing weird shapes in my data
18:28 faceface (not just because of drugs)
18:28 faceface http://imagebin.ca/view/3h7SXLQ7.html
18:28 faceface you ever done tiling?
18:29 deafferret ooooo... if you see the Blessed Mother let me know!
18:29 deafferret no, this doesn't look at all familiar, sorry
18:29 faceface ;-)
18:30 faceface here is the jitterized version: http://imagebin.ca/view/GJ_oxK.html
18:30 faceface perhaps I'll email the list
18:30 faceface Title: werid scenes inside the gold mine
18:31 faceface too late too late...
18:31 faceface have a nice week
19:10 deafferret rbuels: a functional mutate() !  http://github.com/jhannah/sandbo​x/blob/master/erlang/mutate.erl
19:11 johnraekwon left #bioperl
19:30 johnraekwon joined #bioperl
20:14 johnraekwon anyone have any experience with the bioperl script load_interpro.pl
20:15 johnraekwon Documentation is basically non-existent..
20:15 johnraekwon and I cant figure the appropriate command line syntax
20:17 deafferret hey, you're back. didn't see your return
20:18 deafferret I can try to help now
20:19 deafferret how big is load_seqdb_test.txt ?
20:19 johnraekwon ok GREAT!
20:19 johnraekwon some 35kb
20:20 deafferret add, push that  :)
20:20 deafferret add, commit, push
20:20 johnraekwon one sec.
20:20 deafferret time's up!
20:25 johnraekwon looks like i managed
20:26 johnraekwon sorry I am a slow arse
20:26 johnraekwon actually this file name is slightly different
20:26 johnraekwon note... it is load_seqdb_test_dat.txt
20:26 johnraekwon but it is the correct test data
20:32 deafferret installing Data::Stag, whatever that is
20:35 johnraekwon might be plenty o dependencies...
20:35 johnraekwon depending on your module config
20:45 deafferret ok, so it's running and kicking out hashes. what was the problem again?  :)
20:45 johnraekwon hi
20:45 johnraekwon ok
20:45 johnraekwon so, it kicks out 4 interesting fields for me
20:45 johnraekwon the stub does what it is supposed to do
20:45 johnraekwon now
20:46 johnraekwon if you compare that to load_seqdatabase.pl
20:46 johnraekwon you get all the same info (and a lot more) except you dont get the annotation
20:46 johnraekwon interpro optional ID
20:46 johnraekwon which is the domain name
20:46 johnraekwon I would like to make load_seqdatabase.pl give me that info, but not sure how to go about this
20:48 johnraekwon in case I wasnt clear, the stub DOES produce this info on the interpro domain (optional id) but the other script does not...
20:49 johnraekwon in fact, i believe it should (which is clearly a wrong belief), but I think getting it to do so should be minor... but still just over my head
20:51 deafferret so PP2A_B56 is the thing you need?
20:51 johnraekwon for example, yes
20:51 johnraekwon I want to get all of those, along with the other 3 pieces of info into a mysql db
20:52 johnraekwon so, the setup is using bioperl, bioperl-db and biosql
20:52 johnraekwon input is a swissprot .dat file
20:52 johnraekwon of which you have a small excerpt
20:52 deafferret so is IPR002554 working via load_seqdatabase.pl? it puts it in your database somewhere?
20:53 johnraekwon If you pass this file through the script load_seqdatabase, then it take most of the annotations and passes them to mysql
20:53 johnraekwon yes.. that one does pass
20:54 johnraekwon it goes to db_xref
20:54 johnraekwon as expected
20:55 deafferret so where are you expecting PP2A_B56 to end up?
20:56 johnraekwon good question.. one sec
20:56 johnraekwon maybe here: dbxref_qualifier_value
20:56 johnraekwon or, I would happily create a place for them... I just dont even know why this info is not parsed
20:56 johnraekwon being a valid annotation and all
21:06 johnraekwon I am gonna step away for a short while... I'll leave the session burning and check in when I'm back... cool?
21:07 deafferret sure. I should go to this birthday party....
21:07 deafferret hmm... not sure I'm going to be able to debug this w/o actually having a database injection occur
21:07 deafferret so I'd need to set up the database and all
21:08 johnraekwon Yeah, I think that is true...
21:09 johnraekwon ...any chance we could resume on Sunday... or when?
21:09 deafferret struggling to grok the design of  Bio/DB/BioSQL/SeqFeatureAdaptor.pm
21:09 deafferret are you on the bioperl-l mailing list? is there still a bioperl-db mailing list?
21:10 deafferret this is a bioperl-db question, I believe. not bioperl proper
21:10 deafferret can't remember if there's still a separate mailing list
21:10 deafferret I'm jay @ jays . net   if you want to prod me   :)
21:10 johnraekwon there is, and I sent out... but it is being moderated before dissemination
21:11 johnraekwon I dont know if there is a db  mailing list, but will check
21:11 deafferret ah. that MailMan server hates me for some reason
21:11 johnraekwon no shit right!
21:11 deafferret if it's not just me then they need to work on their spam filtering  :)
21:11 johnraekwon OK, will try to find the db list...  thanks for the attention on this matter though
21:12 deafferret sure.   I don't see one. Not sure if bio-sql is the same thing or not
21:13 deafferret been a few years since I touched this stuff
21:13 johnraekwon biosql is just a sort of schema thing
21:14 johnraekwon I feel like an island that is for sure... chose these tools because thought it would be smooth sailing since so much pre-existing code... turns out my simple application is slightly obscure
21:14 deafferret oh, shit. way later.  45m late already gotta run
21:14 deafferret way late   :)
21:14 johnraekwon no worries, peace bro

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