Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-19

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Time Nick Message
03:45 rbuels deafferret: what is getting lost in the round trip?
03:46 * rbuels is not surprised that it doesn't
08:40 kai morning folks
08:47 CIA-95 bioperl-live: Florent Angly master * rbcd98d4 / (7 files in 6 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/aCodbA
08:47 CIA-95 bioperl-live: Florent Angly master * r893390f / (Bio/Root/IO.pm t/Root/RootIO.t): New Bio::Root::IO method to insert text at an arbitrary line in a file - http://bit.ly/ayofbH
10:16 Jun morning~
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10:44 carandraug Hi everyone! I'm a new user of BioPerl and have a quick question whose answer can't find online. How can I get the official symbol of a gene extracted from GenBank?
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14:06 flu perl 6 is 10 years old today (sort of).  http://use.perl.org/~masak/journal/40451
14:08 Jun Hi, carandraug. Check http://www.bioperl.org/wiki/HOWTO:Beginners
14:08 Jun You will find your answer there.
14:10 carandraug Jun, I did read it. I couldn't find it. I also searched the bioperl mailing list. I don't know if it's related but from what I read the official symbol are mantained by HGNC and a mail in the mailing list says that there's no BioPerl module to search HGNC
14:40 Jun Ok, I think you are right. I dont think there is any BioPerl module related with HGNC.
14:40 Jun But there is a similar Perl module from Ensembl, fetching genome annotation information from Biomart. Try that.
14:41 Jun http://www.biomart.org/martservice.html
14:42 flu Also, the HGNC has their own biomart server, http://www.genenames.org/biomart/
14:43 carandraug Jun, flu, thank you both
14:45 flu or just use your extracted GenBank IDs and use http://www.genenames.org/cgi-bin/hgnc_stats.pl to generate a file containing the HGNC symbol.
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16:29 Guest90481 hey
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18:24 deafferret rbuels: the positions are completely gone
18:25 deafferret they seemed to be stored in sqlite , yet the gff dumper somehow fails to write it out
18:25 deafferret which surprised me. I didn't expect it to be perfect, I was shocked that it couldn't do the basics
18:25 rbuels deafferret: wow, i am surprised it's that fundamental a breakage
18:25 deafferret so I rolled my own   :(
18:26 deafferret ya. if you're interested I can write a demo
18:26 rbuels deafferret: yes of course this should go in bugzilla
18:26 deafferret but there seem to be ZERO tests so I retreated
18:26 deafferret rbuels: oh no, I'm not falling for THAT again!
18:26 rbuels deafferret: lincoln probably needs to see it.  also mention that there are zarro toosts
18:26 deafferret The Gay Blade!
18:27 rbuels no no, not toosts, poofs.
18:27 deafferret isn't py[tab] spreading rumors about FeatureIO rewrites or something?
18:27 deafferret in that case, the whole stack is *ignore*  ?
18:27 rbuels oh i dunno.  he talks about it occasionally
18:28 deafferret i was *really* surprised. damn open source
18:28 rbuels deafferret: anyway, file a bug with a test case demonstrating it
18:28 * deafferret spits
18:28 deafferret rbuels: ELAZY
18:28 rbuels file it dammit!
18:28 * deafferret cowers
18:29 rbuels (when i was interning at ibm, a couple of the programmers there called it 'open sores'
18:29 rbuels )
18:29 rbuels haw haw
18:39 deafferret double true
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19:42 carandraug Hi! I need some help if someone has the time. I'm not new to Perl but never used any object programming before. I may be complicating a really simple thing but I can't get a sequence from a gene id. I used get_Seq_by_id method right (I think), and I can use the desc and display_id methods, but when I use the seq method I get nothing. Shouldn't "say  $object->seq;" give me the DNA sequence?
19:52 rbuels carandraug: try bp_fetch.pl net::genbank:AC217914.1
19:52 rbuels carandraug: and if that works for you, have a look at that script to see how it does things
19:55 carandraug rbuels, it works. Got a large DNA sequence
19:55 carandraug rbuels, >gi|169647113|gb|AC217914.1| Solanum lycopersicum chromosome 1 clone C01HBa0033C15, complete sequence
19:56 rbuels carandraug: yep.  so now you can take a look at that script to see how it manages getting the sequence
19:56 rbuels carandraug: also, you can try putting in your own IDs there to make sure it works on them too
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20:04 carandraug rbuels, thanks. I played with it and got a different thing. I think I'm confusing gene ids with access ids. But can you explain why using the seq method didn't got me the dna sequence?
20:06 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | paste to http://pastebin.com/
20:07 rbuels carandraug: i don't really have enough information to guess why.  perhaps use http://pastebin.com/ to paste your code here?
20:09 carandraug rbuels, here it is http://pastebin.com/hkGrSCwD I think it's probably a very simple error
20:11 deafferret carandraug: are you getting a big fat error? or nothing?
20:12 pyrimidine Entrez Gene does not contain sequence information
20:12 pyrimidine never did
20:12 carandraug deafferret, no big error. Just an error of use of uninitialized value
20:12 pyrimidine you need to grab the linked-to GenBank info
20:14 deafferret py[tab]: Are *Feature* classes on the chopping block? Or should I open a ticket on Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS  failing to round-trip feature locations?
20:15 carandraug pyrimidine, you mean I should have used DB::GenBank instead of EntrezGene? I tough get_Seq_by_id would get me the sequence
20:16 pyrimidine deafferret: I would open a ticket, but it might be a good idea to bring it up on the gbrowse list
20:17 deafferret gak. the Email Deprecation League would never forgive me
20:17 pyrimidine :)
20:17 pyrimidine some of us are still old-school
20:17 pyrimidine Feature classes are not on the chopping block, just FeatureIO (and that's to be reimplemented)
20:17 deafferret carandraug: ya, try Bio::DB::GenBank ?
20:17 pyrimidine carandraug: what deafferret said
20:18 deafferret carandraug: congrats! you've discovered an (undocumented?) Entrez feature!  :)
20:18 pyrimidine EntrezGene just gets you a bit more information about that gene, but there is no sequence in the returned XML
20:19 pyrimidine (I guess they consider that lightweight)
20:21 carandraug pyrimidine, I used GenBank but now it changed. Even tough I'm using get_seq_by_id , is giving me a different gene
20:21 carandraug pyrimidine, it's giving me the same as if I were using accession number
20:22 pyrimidine code?
20:24 carandraug pyrimidine, http://pastebin.com/qEVRV8BN
20:24 pyrimidine gene ID != nuc ID
20:25 carandraug pyrimidine, but it's the same id number I was using when using EntrezGene
20:26 pyrimidine I'm getting two different things with this ID
20:26 pyrimidine Gene:
20:26 pyrimidine http://www.ncbi.nlm.nih.gov/gene?term=8970
20:26 pyrimidine nuccore"
20:26 pyrimidine http://www.ncbi.nlm.nih.gov/nuccore/8970
20:27 carandraug pyrimidine, I want the gene
20:27 pyrimidine right.  You need to pull the start/end coordinates from the gene record
20:28 pyrimidine grab the proper nucleotide GI from the record as well
20:28 pyrimidine use that GI to grab the correct record
20:28 pyrimidine use the coordinates to limit to the region you want
20:30 carandraug pyrimidine, hmm... but if I already have the gene ID why isn't it possible to just get their sequences if I want all of it?
20:31 pyrimidine b/c the folks at NCBI decided to make it more difficult
20:31 pyrimidine ;-)
20:31 pyrimidine just the way it is, unfortunately
20:31 pyrimidine that's one of the reasons it doesn't get as much use as ensembl or ucsc
20:33 pyrimidine rbuels: have any idea what happened here? http://search.cpan.org/~mingyiliu/Bi​o-ASN1-EntrezGene-1.10-withoutworldw​riteables/lib/Bio/ASN1/EntrezGene.pm
20:33 pyrimidine (look at the dist name)
20:34 carandraug pyrimidine, oohh! I've been trying to do this all day. I've read about and saw many scripts that wroked by looking into those coordinates. I kept looking because I tought it should be a simpler way, never occurred that they would limit like that. Should I look into ensembl to make things easier then?
20:35 pyrimidine yes, and don't worry about reinstalling the older bioperl
20:35 pyrimidine the latest works for me
20:35 pyrimidine http://www.bioperl.org/wiki/HO​WTO:Getting_Genomic_Sequences
20:35 deafferret pyrimidine: Looks to me like Bio::ASN1 isn't part of BioPerl, so those namespaces aren't reserved, so Mingyi Liu uploaded something to PAUSE and it took it
20:36 carandraug pyrimidine, thanks a lot for your help. You've been most helpful
20:36 pyrimidine right, but what is Bio-ASN1-EntrezGene-1.10-withoutworldwriteables?
20:36 deafferret you can call your package foo.tgz if you want
20:37 pyrimidine :/
20:37 deafferret PAUSE opens it and says, "ok, Foo has Bio::ASN1::* in it... proceeding"
20:37 * deafferret uploads BioPerl-2.7.tgz containing Bio::JAYROCKS::Boogity!.pm
20:37 pyrimidine yes, it's just confusing
20:38 * deafferret agrees
20:38 pyrimidine though, if you attempted that, you would get nasty **UNAUTHORIZED RELEASE** stamped on all the modules
20:38 pyrimidine oh well, at least there's a new version
20:39 pyrimidine carandraug: Note the link I posted (all about pulling down genome coords and seqs)
20:39 pyrimidine includes all the cases mentioned, including ensembl API (though it may be a bit out-of-date)
20:40 deafferret pyrimidine: I would? I didn't know that.
20:40 pyrimidine if it conflicts with an already-registered namespace in Bio::*, yes, then it would be unauthorized acc to CPAN
20:41 deafferret oh, Bio::JAYROCKS is already out there? woot!  ;)
20:41 pyrimidine kurila is a good example (perl fork)
20:41 pyrimidine http://search.cpan.org/~tty/kurila-1.19_0/
20:41 carandraug pyrimidine, I saw the link. Thanks again
20:41 pyrimidine carandraug: np
20:41 * deafferret doesn't see   Mingyi Liu discussing that release http://tinyurl.com/22vm6cn
20:42 deafferret there's ASN.1 conversations back in 2007, but nothing about "I'm going to CPAN this"
20:43 deafferret pyrimidine: re: kurila: yes, but Bio::JAYROCKS would not be flagged "UNAUTHORIZED"
20:43 deafferret so I would pollute up the Bio:: namespace with no flag
20:43 pyrimidine that's true, as long as it had no conflicting namespace issues
20:43 * deafferret nods
20:44 pyrimidine Bio::Phylo does this as well, though Rutger may join the fold at some point
20:45 deafferret re: Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS   I should post to both bioperl-l and the gbrowse list?
20:45 deafferret and open a bugzilla?
20:47 pyrimidine yes, and yes
20:47 pyrimidine I think it would help to get an idea of how much round-tripping can be easily done
20:50 * deafferret tries to drum up yesterday's source for new branch topic/bug_####
21:02 deafferret oh. that does work. it's when I Bio::SeqIO a ensembl file in it doesn't work
21:04 * rbuels slaps his forehead
21:04 deafferret hmm? am I an idiot?
21:04 deafferret a feature slurped from ensembl that Store accepts should kick out gff, right?
21:04 rbuels no, there was a mosquito trying to bite me
21:05 * deafferret slaps rbuels
21:05 deafferret another one!
21:05 deafferret a bot fly!
21:05 rbuels lol
21:05 * deafferret cocoons rbuels in saran wrap for his own protection
21:06 pyrimidine left #bioperl
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21:06 deafferret phew
21:09 deafferret sigh... about to add another 0.8MB to bioperl-live forever
21:10 deafferret or should I clip the 623KB sequence out of here?  -ponder-
21:12 deafferret molesting the sequence might invalidate the complaint... but 800K is awfully big for one bug report.
21:12 deafferret I see zero .ensembl files in t/   I guess I'll add it
21:12 deafferret to master
21:15 rbuels sounds fine to me
21:16 deafferret rbuels: what's your github password? I don't wanna be in the blame log for this one...
21:17 rbuels deafferret: you edited out the sequence to keep down size right?  and made sure there aren't any checksums or length fields in the record that it would screw up?
21:18 deafferret um, no. i left it in there under the theory that other tests might want an .ensembl formatted file too?    find ./ | grep -E '^ID'   shows zero files
21:18 deafferret smaller ones would work too I assume
21:18 * deafferret throws an xargs in there too
21:18 rbuels deafferret: would be nice to have a smaller one instead ...
21:19 * deafferret pouts, complies
21:22 deafferret heh. BRCA2 not a good choice for "small file". way too many documented variants  :)
21:27 deafferret oh, yet again, I am an idiot.
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21:50 deafferret huh. this is different from the behavior yesterday   http://gist.github.com/482081
21:53 deafferret ah, there it is.   $db->no_blobs(1);
21:53 deafferret either way, IT BE BORKED
21:55 deafferret select * From feature_location looks ok
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22:11 deafferret http://bugzilla.open-bio.o​rg/attachment.cgi?id=1526
22:11 deafferret http://bugzilla.open-bio.org/show_bug.cgi?id=3120
22:11 * deafferret goes back to JFDI
22:42 dukeleto joined #bioperl
22:42 dukeleto hola
22:43 * deafferret waves
22:48 dukeleto deafferret: i just submitted this bioperl bug: http://bugzilla.open-bio.org/show_bug.cgi?id=3121 with a patch to fix it and test case
23:06 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * r3819ef7 / Bio/OntologyIO/Handlers/InterProHandler.pm : interpro parser now throws an error when it cannot find the term for an interpro type - http://bit.ly/apJpZX
23:21 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * rd1d9d1a / Bio/Ontology/SimpleOntologyEngine.pm :
23:21 CIA-95 bioperl-live: added a little defensive error checking when adding ontology relationships.
23:21 CIA-95 bioperl-live: throws an error when either subject or object are not defined. also
23:21 CIA-95 bioperl-live: reverts 25403c7fbcdf9364fcc03b5d3a637553011c965a, which allowed this
23:21 CIA-95 bioperl-live: method to succeed in this case. - http://bit.ly/aUvsXM
23:26 dukeleto rbuels++
23:26 deafferret dukeleto: ah, cool. do you have commit?
23:27 dukeleto deafferret: no, i don't have a commit bit yet, if that is what you are asking. I would like one, though.
23:27 * rbuels would add dukeleto, but does not want to mess with learning the github org stuff right now
23:27 deafferret oh... work on this is now going on in topic/leto_interpro_parse
23:27 dukeleto deafferret: yep
23:28 rbuels deafferret: feel free to add him as a committer if you know how to work that newfangled stuff
23:28 deafferret hmm.... is it this button?
23:28 rbuels owww now
23:28 rbuels no
23:28 rbuels that's the eject button
23:28 deafferret oh, bummer. joke fail
23:28 rbuels that ejects ... a botfly larva from my scalp!
23:28 deafferret lucky bastard
23:28 deafferret not sure what I typod on that hilarious /kick
23:29 rbuels haha
23:29 rbuels that would have been funny
23:29 dukeleto mmmmmm botfly larva
23:30 deafferret I do not have the "admin" button   http://github.com/bioperl/bioperl-live
23:30 deafferret ELACKOFCOOL
23:30 deafferret dukeleto: so do you have a bioperl-live fork you can apply all that cool stuff to?
23:31 dukeleto deafferret: yes, i have a bioperl-live fork at http://github.com/leto/bioperl-live
23:32 deafferret cool. so if you apply your patches to that fork then I can pull it into the main bioperl-live
23:32 * rbuels learns how to work the newfangled thing
23:32 deafferret assuming you've taken all that bug report feedback into account appropriately
23:32 deafferret rbuels: do you have an "admin" button on that URL?
23:32 rbuels deafferret: yeah
23:32 rbuels dukeleto: you are now on the 'BioPerl Team'
23:32 deafferret oh. then click it, click collaborators, and add him
23:32 rbuels deafferret: no no!  get with the times!
23:33 rbuels deafferret: this is the Organizations Era on github!
23:33 dukeleto rbuels: danke
23:33 was kicked by deafferret: ?
23:33 rbuels joined #bioperl
23:33 rbuels do not eject me from the temple!
23:33 deafferret huh... Freenode doesn't like long winded kick messages apparently
23:33 rbuels i have come to show you the error of your ways!
23:33 dukeleto rbuels: you going to write a test for the InterProHandler code change? or should I?
23:33 deafferret LESSON LEARNED
23:33 dukeleto rbuels: also, where is the bioperl perltidy conf?
23:34 rbuels dukeleto: in maintenance/
23:34 * rbuels does not like that name much
23:34 deafferret dukeleto: so are you in branch   topic/leto_interpro_parse
23:34 deafferret doing your coolness?
23:35 dukeleto rbuels: we should probably make solgenomics an organization, so we can get the spiffy "switch context" button for SGN-related repos
23:35 rbuels dukeleto: yes i agree
23:35 dukeleto deafferret: i will make all relevant changes to the topic/leto_interpro_parse branch
23:36 CIA-95 bioperl-live: Florent Angly master * r3cde0be / (Bio/Root/IO.pm t/Root/RootIO.t):
23:36 CIA-95 bioperl-live: Bio::Root::IO->_insert() special case when inserting at first line of
23:36 CIA-95 bioperl-live: an empty file - http://bit.ly/9MECi0
23:36 CIA-95 bioperl-live: Florent Angly master * r8ecdf90 / Bio/Assembly/IO/ace.pm : Improved Bio::Assembly::IO::ace->write_header - http://bit.ly/czQk3F
23:38 dukeleto who does the bioperl twitter account? it has been dormant for a while
23:38 rbuels dukeleto: erm...pytab i think
23:38 rbuels dukeleto: i mean ...
23:39 * rbuels laboriously types
23:39 rbuels dukeleto: pyrimidine
23:39 * rbuels laughs uproariously at the running joke
23:45 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * rf1f67ab / t/Ontology/Ontology.t : more perltidy -
23:45 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * r99d5804 / Bio/OntologyIO/Handlers/InterProHandler.pm : more perltidy -
23:45 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * rcd2c477 / Bio/OntologyIO/Handlers/InterProHandler.pm :
23:45 CIA-95 bioperl-live: added 'Region' interpro type. recently-added test from leto now passes.
23:45 CIA-95 bioperl-live: this type was added in InterPro release 19.0, according to http://www.ebi.ac.uk/interpro/tutorial.html -
23:46 dukeleto if i want to improve a test or fix a typo, can I commit that to master? or does that need a topic branch?
23:46 rbuels dukeleto: no, that can go to master
23:46 dukeleto rbuels: cool
23:46 dukeleto that CIA announcement has no tinyurl
23:47 rbuels i don't think it's going through github
23:47 rbuels pytab should probably take a look at that
23:48 * dukeleto can hear rbuels attempting to laboriously type
23:48 * rbuels grunts
23:53 rbuels dukeleto: are you adding any tests?
23:55 CIA-95 bioperl-live: Robert Buels topic/leto_interpro_parse * rc08e274 / t/Ontology/OntologyEngine.t : more perltidy - http://bit.ly/dypWT6
23:56 dukeleto rbuels: i will add a test for interprohandler
23:57 rbuels dukeleto: well, that's being tested by the interpro parsing thing already, kind of.  and it's going to be kind of hard to test
23:57 rbuels dukeleto: it might be easier and more useful to add a test for it dieing if you try to add a relationship with no subject or object
23:58 rbuels dukeleto: to t/Ontology/OntologyEngine.t maybe
23:58 rbuels or t/Ontology/Ontology.t
23:58 rbuels probably t/Ontology/Ontology.t would be better

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