| Time |
S |
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~ |
| 10:29 |
|
|
carandraug joined #bioperl |
| 10:39 |
|
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carandraug_ joined #bioperl |
| 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? |
| 11:18 |
|
|
jhamilton joined #bioperl |
| 13:01 |
|
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genehack joined #bioperl |
| 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. |
| 16:28 |
|
|
AMIR joined #bioperl |
| 16:29 |
|
Guest90481 |
hey |
| 18:23 |
|
|
bag joined #bioperl |
| 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 |
| 19:38 |
|
|
brandi joined #bioperl |
| 19:38 |
|
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brandi left #bioperl |
| 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 |
| 19:59 |
|
|
pyrimidine joined #bioperl |
| 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/~mingyi[…]SN1/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[…]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 |
| 21:06 |
|
|
pyrimidine joined #bioperl |
| 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. |
| 21:45 |
|
|
brandi joined #bioperl |
| 21:45 |
|
|
brandi left #bioperl |
| 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 |
| 21:57 |
|
|
pyrimidine left #bioperl |
| 22:11 |
|
deafferret |
http://bugzilla.open-bio.org/a[…]hment.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 |
