| Time |
Nick |
Message |
| 11:33 |
* kai |
waits for pyr[tab] to wake up |
| 13:12 |
|
brandi joined #bioperl |
| 13:12 |
|
brandi left #bioperl |
| 15:40 |
deafferret |
py[tab] WAKEY WAKEY! |
| 15:41 |
deafferret |
12:20 <@pyrimidine> deafferret: email defamer |
| 15:41 |
deafferret |
:) |
| 15:45 |
kblin |
hehe |
| 15:45 |
kblin |
still at yapc? |
| 15:48 |
deafferret |
nah, back on thr :) |
| 16:12 |
|
XaeroOne joined #bioperl |
| 16:29 |
|
wizi joined #bioperl |
| 16:30 |
wizi |
hello? |
| 16:41 |
|
wizi joined #bioperl |
| 16:41 |
wizi |
hello? |
| 16:47 |
wizi |
anyone here? |
| 16:47 |
XaeroOne |
they are here but will have to wait |
| 16:52 |
wizi |
thanks |
| 16:54 |
kblin |
and also ask whatever you want to ask |
| 16:54 |
kblin |
apart from "anybody here?" |
| 16:55 |
wizi |
sorry i am new here |
| 16:55 |
wizi |
i just want to ask if Bioperl suppose BLAT? |
| 16:55 |
wizi |
and where can I find the examples? |
| 17:04 |
flu |
http://doc.bioperl.org/bioperl-live/Bio/Tools/Blat.html |
| 17:09 |
wizi |
my $obj = Bio::Tools::Blat->new(-fh=>$filehandle); (what is filehandle, my database or my queries?) |
| 17:10 |
wizi |
and what is the differnet between filehandle and filename? |
| 17:10 |
wizi |
different* |
| 17:19 |
rbuels |
wizi: a filename is a string with the name of the file, a filehandle is a filehandle. you should read a book about programming perl. |
| 17:20 |
deafferret |
rbuels should too |
| 17:21 |
deafferret |
:) rbuels: did you miss me? |
| 17:23 |
wizi |
there are 2 paras for Blat-> new: filename and filehandler, i am just wondering which is my query file and which is my database. Sorry i am new to bioperl |
| 17:25 |
deafferret |
looks like you use one or the other. give it a filename, or give it a filehandle (where you've already opened that filename for read) |
| 17:25 |
deafferret |
your choice |
| 17:33 |
|
dnewkirk joined #bioperl |
| 17:39 |
* deafferret |
does a silly dance trying to get rbuels' attention |
| 17:39 |
rbuels |
eh what |
| 17:40 |
deafferret |
you coming to YAPC::NA::2011? |
| 17:40 |
rbuels |
oh stop it! i have to get the new repeats set into the ITAG pipeline and get the new tomato release going through it |
| 17:40 |
rbuels |
i don't know yet, too far away |
| 17:40 |
deafferret |
Ah, the Pittsburgh Heinz goons are threatening you? |
| 17:40 |
rbuels |
lol |
| 17:41 |
rbuels |
no heinz is so far down the food chain, they are not involved |
| 17:41 |
rbuels |
we just happen to be using the Heinz 1706 tomato as our reference |
| 17:41 |
rbuels |
that's the one they use in their ketchup. |
| 17:41 |
deafferret |
wut? aren't they like the largest corporate interest in tomatoes on the planet? |
| 17:42 |
dnewkirk |
they use tomatoes in the ketchup? |
| 17:42 |
deafferret |
dnewkirk: they flavor the corn syrup with real tomatoes, yes |
| 17:43 |
deafferret |
YAPC::NA::2009 toured Heinz field in Pittsburgh :) |
| 17:43 |
deafferret |
with the crazy 50 foot long celebratory ketchup-pouring thing when they score |
| 18:00 |
|
faceface1 joined #bioperl |
| 18:00 |
|
dnewkirk joined #bioperl |
| 18:00 |
|
wizi joined #bioperl |
| 18:00 |
|
XaeroOne joined #bioperl |
| 18:00 |
|
kblin joined #bioperl |
| 18:00 |
|
flu joined #bioperl |
| 18:00 |
|
kai joined #bioperl |
| 18:00 |
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deafferret joined #bioperl |
| 18:00 |
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rbuels joined #bioperl |
| 18:01 |
deafferret |
wizi: no, they're not the same :) |
| 18:01 |
deafferret |
read the POD of each, they describe what they do |
| 18:01 |
deafferret |
Bio::Tools::Blat parses BLAT files. those other things run things |
| 18:02 |
deafferret |
(I assume) |
| 18:06 |
|
driley joined #bioperl |
| 18:07 |
|
faceface joined #bioperl |
| 18:22 |
CIA-95 |
bioperl-live: Chris Fields topic/species_proxy * r1687dce / Bio/Species.pm : Bio::Species delegates to Bio::Taxon and Bio::Tree::Tree; this removes the need for weaken() as Bio::Species just acts as a proxy class. Needs further testing to ensure no mem leaks persist - http://bit.ly/bV8s77 |
| 18:22 |
deafferret |
purl: rbuels is also King of the Veggie Tales |
| 18:22 |
rbuels |
web services and data federation! |
| 18:22 |
deafferret |
that's what I said |
| 18:24 |
deafferret |
purl: rbuels also services The Federation |
| 18:24 |
rbuels |
right. |
| 18:53 |
CIA-95 |
bioperl-live: Chris Fields topic/species_proxy * r5cba9a6 / Bio/Species.pm : remove code refs for index tests, a few doc changes and comments - http://bit.ly/c0Ms5u |
| 19:02 |
|
pyrimidine joined #bioperl |
| 19:07 |
CIA-95 |
bioperl-live: Chris Fields topic/species_proxy * r9ca1de9 / (t/SeqIO/Handler.t t/SeqIO/swiss.t): bit premature to check for this (API indicates this should be the more general Bio::Species until we deprecate it) - http://bit.ly/b91Ur5 |
| 19:48 |
kblin |
pyrimidine: hey there |
| 19:48 |
pyrimidine |
o/ |
| 19:49 |
kblin |
pyrimidine: tom's tests still print out results fine, so I figure they're covered |
| 19:49 |
kblin |
so from my point of view bioperl-hmmer3 can be removed |
| 19:49 |
pyrimidine |
ok |
| 19:49 |
deafferret |
py[tab]!! hi! :) |
| 19:49 |
pyrimidine |
will post to the list on that |
| 19:50 |
pyrimidine |
deafferret: hi right back at ya |
| 19:50 |
* deafferret |
swoons |
| 20:05 |
* kblin |
sighs |
| 20:05 |
kblin |
#bioinformatics is lots and lots of off-topic chatter |
| 20:07 |
deafferret |
kblin: did you see the US vs. Ghana game? hoo-doggies! |
| 20:10 |
kblin |
deafferret: nope, I didn't even see England vs. Germany |
| 20:11 |
deafferret |
kblin: that was an "off topic" joke :) |
| 20:11 |
kblin |
yeah, I realized |
| 20:11 |
kblin |
about at the moment when I hit enter |
| 20:11 |
* deafferret |
moves kblin's jaw to simulate laughter |
| 20:11 |
* deafferret |
laughs along with kblin |
| 20:12 |
kblin |
by just moving your jaw? I'd love to see _that_ |
| 20:12 |
kblin |
:D |
| 20:13 |
deafferret |
centuries of ventriliquism |
| 21:05 |
flu |
rbuels, any idea what is going on with this simple shipwright import? http://pastebin.com/Bzd6mR4j |
| 21:06 |
* rbuels |
looks |
| 21:06 |
rbuels |
that's not shipwright, it's your cpan that's borking. |
| 21:06 |
rbuels |
perhaps it doesn't like running under shipwright. |
| 21:07 |
flu |
hrmm |
| 21:07 |
rbuels |
i'd recommend disabling CPAN::SQLite |
| 21:07 |
rbuels |
it's always been very questionable for me. |
| 21:08 |
rbuels |
flu: cpan[1]> o conf use_sqlite 0 |
| 21:09 |
flu |
that did it |
| 21:09 |
* flu |
tips his hat to rbuels once again |
| 21:09 |
|
summatusmentis joined #bioperl |
| 21:16 |
summatusmentis |
hi all, I have some... conceptual questions about how this all works |
| 21:16 |
pyrimidine |
42 |
| 21:17 |
summatusmentis |
I'm wondering about using BioPerl in a context that isn't biology, but what my problem amounts to is I've got sequences of numbers |
| 21:17 |
summatusmentis |
that I'm looking to compare, and either show that they're similar, or show where the differences are |
| 21:17 |
pyrimidine |
Array::Compare? |
| 21:18 |
summatusmentis |
umm... I have no idea? Is that perl? |
| 21:18 |
kblin |
yeah |
| 21:18 |
kblin |
check CPAN :) |
| 21:18 |
summatusmentis |
I have a rough working knowledge of perl, so... |
| 21:18 |
summatusmentis |
hah, right |
| 21:18 |
pyrimidine |
List::Compare as well |
| 21:19 |
summatusmentis |
oh, that's simple comparison. unfortunately my life isn't that easy |
| 21:19 |
* pyrimidine |
is sad no one got the '42' joke |
| 21:19 |
pyrimidine |
summatusmentis: code example? (use gist.github.com) |
| 21:20 |
summatusmentis |
pyrimidine: I haven't started coding with bioperl yet, I'm kinda trying to figure out if it's worth my time to try and get it to fit my problem |
| 21:21 |
pyrimidine |
saying this as a perl prog and a bioperl core dev, if it isn't biologically relevant it probably not isnworth using bioperl |
| 21:21 |
pyrimidine |
*isn't worth |
| 21:22 |
pyrimidine |
an explanation of the problem might help, though |
| 21:22 |
summatusmentis |
sure, I can do that |
| 21:22 |
summatusmentis |
my "full traces" are lists of chunk requests, from startup to login of VMs |
| 21:23 |
summatusmentis |
the overall goal is to show that on the block level, chunk requests for boot time (for the time being) are fairly consistent and ordered |
| 21:24 |
summatusmentis |
so what this means is either "traces are the same" (which they aren't) or "traces have subsequences that are the same) |
| 21:24 |
summatusmentis |
which manually comparing seems to suggest there are subsequences that are consistent |
| 21:25 |
summatusmentis |
based on the reading I've done, it looks like bioperl is pretty biologically based, but might be able to be wrangled to fit this problem, given that (again, as I understand it), the abstract problem is the same? |
| 21:28 |
pyrimidine |
this almost seems like something you would use a B-Tree or R-Tree for |
| 21:29 |
summatusmentis |
so then, can I ask, what is it bioperl gets the biologically inclined? |
| 21:30 |
pyrimidine |
the only thing within bioperl that would probably fit something like this is Bio::Range, but I'm pretty sure (99.99%) this isn't what you want |
| 21:31 |
pyrimidine |
summatusmentis: 'biologically inclined?' It's bioperl, the name is pretty self-explanatory. |
| 21:31 |
summatusmentis |
let me rephrase that |
| 21:31 |
summatusmentis |
I know it's bioperl |
| 21:32 |
summatusmentis |
but is the purpose "help find sequences" or is the purpose "expose data in a way that's useful to perl" ? |
| 21:33 |
pyrimidine |
For bioperl, that should be qualified as 'biological sequences', but it's not just that. |
| 21:33 |
dnewkirk |
It's "format data in a useful manner to use in downstream analysis," more or less... |
| 21:33 |
pyrimidine |
dnewkirk++ |
| 21:33 |
summatusmentis |
ah |
| 21:34 |
summatusmentis |
then yes, you're probably right that bioperl won't help me a whole lot |
| 21:34 |
pyrimidine |
I'm thinking what you describe would fit within the B-Tree/R-Tree type of search |
| 21:34 |
summatusmentis |
I think I'm at the downstream analysis stage, and given that I'm not using biological data, it's sorta moot |
| 21:35 |
summatusmentis |
I'll definitely look into those, thanks |
| 21:35 |
summatusmentis |
manual comparison bites, so, you know :) |
| 21:36 |
pyrimidine |
perl implementations are on CPAN. But it's probably worth looking into the various DB implementations (SQLite, mysql, Pg, BDB, etc) |
| 21:38 |
CIA-95 |
bioperl-live: Chris Fields topic/species_proxy * r04253fe / t/Species.t : add test for mem leak (may have to be modified) - http://bit.ly/dB8AVl |
| 21:38 |
summatusmentis |
the reason I ended up here is when googling things like "sequence analysis" and "sequence comparison" bioinformatics seemed to be where all this work was being done |
| 21:39 |
summatusmentis |
but I really appreciate the help, and I'll checkout the B-Tree/R-Tree stuff |
| 21:39 |
pyrimidine |
ok |
| 21:40 |
summatusmentis |
thanks again. tah |
| 21:40 |
summatusmentis |
.wc |
| 21:40 |
|
summatusmentis left #bioperl |
| 21:41 |
CIA-95 |
bioperl-live: Chris Fields topic/species_proxy * r457ad89 / (4 files in 2 dirs): clean up cleaning up (e.g. DESTROY properly) - http://bit.ly/bagP2G |
| 21:42 |
|
wizi joined #bioperl |
| 21:55 |
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newtobioperl joined #bioperl |
| 21:59 |
newtobioperl |
why dont we support BLAT? |
| 21:59 |
pyrimidine |
we do |
| 22:00 |
pyrimidine |
at least, last I heard we did |
| 22:00 |
newtobioperl |
you mean this http://doc.bioperl.org/bioperl-live/Bio/Tools/Blat.html#SYNOPSIS |
| 22:00 |
newtobioperl |
its just a parser |
| 22:00 |
pyrimidine |
right |
| 22:00 |
pyrimidine |
do you mean a wrapper? |
| 22:00 |
newtobioperl |
No Bio::Tools::Blat - parser for Blat program |
| 22:01 |
newtobioperl |
do we have a wrapper? |
| 22:01 |
newtobioperl |
for Blat? |
| 22:01 |
pyrimidine |
have you tried Bio::SearchIO |
| 22:01 |
pyrimidine |
(as the parser)? |
| 22:03 |
newtobioperl |
do you have any document or guide showing you how to use SearchIO Blat? |
| 22:03 |
pyrimidine |
Looks like the wrapper is Bio::Tools::Run::Alignment::Blat |
| 22:04 |
newtobioperl |
I just check it on CPAN, Bio::Tools::Run::Alignment::Blat is not there anymore |
| 22:04 |
pyrimidine |
it's not in BioPerl, it's in BioPerl-run |
| 22:04 |
newtobioperl |
oh |
| 22:04 |
pyrimidine |
http://search.cpan.org/dist/BioPerl-Run/lib/Bio/Tools/Run/Alignment/Blat.pm |
| 22:05 |
newtobioperl |
oh i didnt install that package, thats why |
| 22:05 |
pyrimidine |
The SearchIO format 'blast' will parse BLAT according to the POD |
| 22:05 |
pyrimidine |
there is also 'axt' and 'psl' parsers |
| 22:05 |
pyrimidine |
gotta go |
| 22:06 |
|
pyrimidine left #bioperl |
| 22:13 |
newtobioperl |
How can I install BioPerl-Run 1.6.1 using Perl Package Manager. I am running window 7 and using ActivePerl |
| 22:17 |
rbuels |
newtobioperl: you might consider using strawberry perl, i think it comes with bioperl included. but, see http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows |
| 22:17 |
rbuels |
newtobioperl: in general, there are a lot of questions that will be answered on the wiki |
| 22:18 |
rbuels |
newtobioperl: that wiki page has instructions for ppm installs |
| 22:18 |
newtobioperl |
i followed the ppm installs |
| 22:18 |
newtobioperl |
and i was able to install Bioperl |
| 22:18 |
newtobioperl |
on Cppan |
| 22:19 |
newtobioperl |
but Bioperl-run is not there |
| 22:19 |
newtobioperl |
I am looking for the Repository of BioPerl-Run |
| 22:21 |
rbuels |
newtobioperl: i'm not sure, i have never used perl on windows, you might try looking at the Beyond the Core section on that page: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Beyond_the_Core |
| 22:22 |
rbuels |
newtobioperl: probably you could infer something from the instructions for installing bioperl-db (which is similar to bioperl-run) |
| 22:22 |
rbuels |
newtobioperl: beyond that, i don't know anything, the mailing list would be the place to go. |
| 22:23 |
newtobioperl |
thanks rbuels |
| 22:35 |
dnewkirk |
either strawberry perl or cygwin would work |
| 22:40 |
newtobioperl |
i am trying to install it manually |
| 22:40 |
newtobioperl |
using CPAN |
| 22:50 |
dnewkirk |
If something doesn't work in the way you need it to, you can use git on windows to grab the live version |
| 22:51 |
dnewkirk |
strawberry should be able to install it from a local dir and you'd be good to go. |
| 22:55 |
newtobioperl |
hi dnewkirk, it doesnt work |
| 22:55 |
newtobioperl |
test failed for CPAN installer |
| 22:55 |
dnewkirk |
hmm |
| 22:56 |
newtobioperl |
ill try Git |
| 22:56 |
dnewkirk |
which version of strawberry are you using, just out of curiosity? |
| 22:57 |
newtobioperl |
i am using Activeperl |
| 22:57 |
newtobioperl |
on window 7 |
| 22:57 |
dnewkirk |
ahhh, right, sorry |
| 22:58 |
newtobioperl |
I installed BioPerl using Perl Package Manager |
| 22:58 |
newtobioperl |
(very easy) |
| 22:58 |
dnewkirk |
yep |
| 22:58 |
newtobioperl |
but Bioperl-run is not there |
| 22:58 |
dnewkirk |
That was a nice addition they made recently |
| 22:58 |
newtobioperl |
do you know how I can run GIT on window |
| 22:58 |
newtobioperl |
? |
| 22:59 |
newtobioperl |
all I want to do is BLAT |
| 23:00 |
dnewkirk |
lemme get on a windows box and check a couple things |
| 23:10 |
dnewkirk |
are you building it in the command prompt from cpan directly? |
| 23:12 |
newtobioperl |
yes |
| 23:12 |
newtobioperl |
but it failed |
| 23:12 |
newtobioperl |
i just installed GIT |
| 23:12 |
newtobioperl |
but i still dont understand the whole Git thing |
| 23:12 |
newtobioperl |
i am running GIt Gui -->clone "http://github.com/bioperl/bioperl-run.git" |
| 23:13 |
dnewkirk |
ok, so that dumps everything into a directory, and you'll build from that directory similar n downloading a file from cpan |
| 23:14 |
newtobioperl |
yes i see all the file in the target directory |
| 23:15 |
newtobioperl |
now what? |
| 23:16 |
newtobioperl |
so I have to do the whole CPAN installation again? |
| 23:16 |
dnewkirk |
no, use "perl Build.PL" |
| 23:16 |
dnewkirk |
assuming that n/dmake is in your path |
| 23:18 |
dnewkirk |
then make with dmake, make test, etc. |
| 23:18 |
newtobioperl |
dmake? |
| 23:19 |
dnewkirk |
part of mingw |
| 23:20 |
newtobioperl |
fail |
| 23:20 |
newtobioperl |
i typed "perl |
| 23:20 |
newtobioperl |
"perl Build.pl" |
| 23:20 |
dnewkirk |
what is the error returned? |
| 23:20 |
newtobioperl |
got "Possible Missing or corrupt "MANIFEST" file |
| 23:21 |
newtobioperl |
"Nothing to enter for 'provides' field in metafile" |
| 23:21 |
newtobioperl |
"creating new 'Build' script for Bioperl-Run version 1.006900 |
| 23:22 |
newtobioperl |
OH THIS IS the error I got right after I typed "perl Build.pl" |
| 23:23 |
newtobioperl |
Bio::Root::Version (1.006001) is installed, but we need version >= 1.006900 |
| 23:24 |
newtobioperl |
where can I get Bio::Root? |
| 23:25 |
dnewkirk |
you may need to install the latest version of Bioperl to get the Bioperl-run to work then |
| 23:25 |
dnewkirk |
Didn't think of that, my apologies |
| 23:25 |
dnewkirk |
Did the original fail to compile when you tried to install it from CPAN? |
| 23:25 |
dnewkirk |
Or was it some sort of other error? |
| 23:26 |
newtobioperl |
I used Perl Manager to Install Bioperl |
| 23:26 |
newtobioperl |
and the Bioperl version is 1.6.1 |
| 23:26 |
newtobioperl |
I believe it is the lastest one |
| 23:26 |
newtobioperl |
right? |
| 23:27 |
deafferret |
that's the latest official release, yes |
| 23:27 |
dnewkirk |
its the latest full release. The live (git) version has updated code that the live (git) version of the bioperl-run module may require |
| 23:28 |
newtobioperl |
I am trying to install Bioperl-live |
| 23:28 |
newtobioperl |
using git |
| 23:28 |
newtobioperl |
lets see what happen |
| 23:36 |
dnewkirk |
dmake isn't playing nice with installing one of the prereqs for bioperl on my xp machine |
| 23:36 |
dnewkirk |
You may be having a similar problem |
| 23:38 |
newtobioperl |
hopefully, ill get it working |
| 23:38 |
newtobioperl |
sigh |
| 23:38 |
newtobioperl |
i haven been spending all day to install this bio-run |
| 23:39 |
newtobioperl |
if its not working, do you think I should uninstall Active perl and go to Strawberry instead? |
| 23:43 |
dnewkirk |
The DB_FIle-1.820 requirement can't be compiled properly, nor can it find a checksum for it (and this is what causes everything to fail) |
| 23:43 |
dnewkirk |
hmm |
| 23:45 |
dnewkirk |
give me ten minutes to test it out and I'll let you know before you waste your time |
| 23:48 |
deafferret |
switch to linux. works great :) |
| 23:52 |
newtobioperl |
thank you so much dnewkirk |
| 23:54 |
newtobioperl |
lol what is the best software that allows you to run dual OS: window and linux? |
| 23:54 |
deafferret |
no clue. I'm addicted to OSX as my desktop and linux servers |
| 23:59 |
dnewkirk |
you can run a vm of linux in windows, if you need windows for most of your work |
| 23:59 |
newtobioperl |
but vm of linux is prob very slow to do Blast, blat |
