| Time |
S |
Nick |
Message |
| 00:00 |
|
deafferret |
PERL5LIB is built into perl |
| 00:00 |
|
Emos |
ah ok |
| 00:07 |
|
Emos |
I think I finally got it installed |
| 00:07 |
|
deafferret |
I give up. Send http://github.com/jhannah/sand[…]r/emos/ensembl.pl to ensembl-dev, see if they can tell you |
| 00:07 |
|
Emos |
why are you giving up? |
| 00:08 |
|
Emos |
didn't you already accomplish the task? |
| 00:08 |
|
Emos |
I thought you found a way of annotating |
| 00:08 |
|
deafferret |
cause I've blindly tried 25 things, none of them work, and this isn't a bioperl problem :) |
| 00:08 |
|
deafferret |
nope. I can't fetch NT_025741.15 which is what you need |
| 00:08 |
|
Emos |
I mean |
| 00:08 |
|
Emos |
it's ok $slice = $slice_adaptor->fetch_by_region( 'chromosome', '20', 100000, 101000 ); |
| 00:09 |
|
deafferret |
yup. that works. but you don't want chr20, you want NT_025741.15 :) |
| 00:09 |
|
Emos |
ok, but then if I can insert instead of 'chromosome', '20', 100000, 101000 |
| 00:10 |
|
Emos |
the variables from the script my $db = new Bio::DB::EntrezGene; |
| 00:10 |
|
Emos |
that you managed this morning |
| 00:10 |
|
Emos |
I'm ok |
| 00:10 |
|
deafferret |
right. and the first example is NT_025741.15, which you cannot map to anything |
| 00:11 |
|
Emos |
I mean I need a general way to look up |
| 00:11 |
|
Emos |
from an ensembl code |
| 00:11 |
|
Emos |
the sequence of the gene and its flankng regions |
| 00:12 |
|
deafferret |
yup. entrezID 54806 -> NT_025741.15 -> FAIL |
| 00:12 |
|
Emos |
BUT, if we don't care about the contig a I don't care, we can work only on sequence |
| 00:13 |
|
Emos |
entrez ID-> position -> add 100kb at each side->get the sequence |
| 00:13 |
|
deafferret |
do you know which chr you're on? |
| 00:13 |
|
Emos |
we must ask the first script |
| 00:13 |
|
Emos |
http://pastebin.com/d51544b65 |
| 00:19 |
|
Emos |
http://doc.bioperl.org/release[…]/DB/BioFetch.html |
| 00:24 |
|
deafferret |
this works: http://github.com/jhannah/sand[…]/master/emos/x.pl |
| 00:24 |
|
deafferret |
you have a bunch of Entrez IDs? |
| 00:25 |
|
Emos |
yes |
| 00:25 |
|
deafferret |
give me the next 2 |
| 00:26 |
|
Emos |
damn |
| 00:26 |
|
Emos |
Can't locate DBD/mysql.pm in @INC |
| 00:26 |
|
Emos |
wait a moment |
| 00:27 |
|
Emos |
I give you what you ask |
| 00:28 |
|
Emos |
27185, 1815, 280730 |
| 00:28 |
|
Emos |
for example |
| 00:29 |
|
Emos |
581 |
| 00:30 |
|
Emos |
what is DBD? |
| 00:30 |
|
deafferret |
database driver |
| 00:30 |
|
Emos |
how to install it? with fink? |
| 00:31 |
|
deafferret |
cpan DBD::mysql |
| 00:33 |
|
deafferret |
boo-ya. this is 100% what you wanted... i think... http://github.com/jhannah/sand[…]/master/emos/x.pl |
| 00:33 |
|
deafferret |
jhannah klab:~/src/sandbox/emos$ perl x.pl |
| 00:33 |
|
deafferret |
54806 chr6 39674566..40088359 |
| 00:33 |
|
deafferret |
27185 chr1 25180339..25794796 |
| 00:33 |
|
deafferret |
1815 chr11 477304..680702 |
| 00:33 |
|
deafferret |
280730 chr18 316898..520907 |
| 00:33 |
|
deafferret |
581 chr19 21626334..21833272 |
| 00:34 |
|
Emos |
WONDERFUL!! |
| 00:35 |
|
Emos |
but I cannot make it work here |
| 00:35 |
|
Emos |
wait a minute |
| 00:35 |
|
Emos |
Can't locate Bio/EnsEMBL/Registry.pm in @INC |
| 00:36 |
|
deafferret |
add that use lib line I mentioned above |
| 00:36 |
|
deafferret |
or perl -I |
| 00:36 |
|
Emos |
echo $PERL5LIB |
| 00:36 |
|
Emos |
/sw/lib/perl5:/sw/lib/perl5/darwin |
| 00:37 |
|
Emos |
I had added all the things to PERL5LIB before |
| 00:37 |
|
Emos |
but now they are gone |
| 00:37 |
|
Emos |
did I have to save them? |
| 00:37 |
|
deafferret |
use lib "/Users/yourusername/src/ensembl/modules"; in your prog |
| 00:38 |
|
Emos |
this doesn't work |
| 00:38 |
|
Emos |
use" not allowed in expression at prova line 8, at end of line |
| 00:39 |
|
deafferret |
you must have a typo |
| 00:40 |
|
Emos |
now |
| 00:40 |
|
Emos |
echo $PERL5LIB |
| 00:40 |
|
Emos |
/sw/lib/perl5:/sw/lib/perl5/darwin:$/Users/EmanueleO/src/bioperl-live:$/Users/EmanueleO/src/ensembl/modules:$/Users/EmanueleO/src/ensembl-compara/modules:$/Users/EmanueleO/src/ensembl-variation/modules |
| 00:41 |
|
deafferret |
those $ are bad |
| 00:41 |
|
deafferret |
add use lib "/Users/EmanueleO/src/ensembl-compara/modules"; # to your prog |
| 00:43 |
|
Emos |
echo $PERL5LIB |
| 00:43 |
|
Emos |
/sw/lib/perl5:/sw/lib/perl5/darwin:$/Users/EmanueleO/src/bioperl-live:$/Users/EmanueleO/src/ensembl/modules:$/Users/EmanueleO/src/ensembl-compara/modules:$/Users/EmanueleO/src/ensembl-variation/modules:/Users/EmanueleO/src/bioperl-live:/Users/EmanueleO/src/ensembl/modules:/Users/EmanueleO/src/ensembl-compara/modules:/Users/EmanueleO/src/ensembl-variation/modules |
| 00:43 |
|
deafferret |
ls -al /Users/EmanueleO/src/ensembl-compara/modules/Bio/EnsEMBL/Registry.pm |
| 00:44 |
|
Emos |
no such file or drectory |
| 00:45 |
|
deafferret |
add use lib "/Users/EmanueleO/src/ensembl/modules"; # to your prog |
| 00:45 |
|
deafferret |
(no -compara) |
| 00:45 |
|
deafferret |
assuming that's where you put Bio/EnsEMBL/Registry.pm |
| 00:46 |
|
deafferret |
I only downloaded ensembl. I didn't do the other 4 |
| 00:46 |
|
Emos |
Can't locate object method "load_registry_from_db" via package "Bio::EnsEMBL::Registry" (perhaps you forgot to load "Bio::EnsEMBL::Registry"?) at prova line 14. |
| 00:47 |
|
deafferret |
do you have the use Bio::EnsEMBL::Registry; line at the top like I do? |
| 00:47 |
|
Emos |
because I commented use Bio::Ensembl::Registry |
| 00:47 |
|
* deafferret |
pokes Emos |
| 00:47 |
|
Emos |
but if I uncomment it |
| 00:48 |
|
Emos |
Compilation failed in require at prova line 8. |
| 00:48 |
|
Emos |
BEGIN failed--compilation aborted at prova line 8. |
| 00:48 |
|
deafferret |
that makes no sense. nopaste your code |
| 00:48 |
|
deafferret |
http://pastebin.com/ |
| 00:48 |
|
deafferret |
copy/paste error? http://github.com/jhannah/sand[…]/master/emos/x.pl |
| 00:50 |
|
Emos |
Can't locate DBD/mysql.pm in @INC |
| 00:50 |
|
deafferret |
where the *bleep* are you trying to use mysql? |
| 00:51 |
|
Emos |
wait a momento |
| 00:53 |
|
Emos |
http://pastebin.com/d1ed79fde |
| 00:54 |
|
deafferret |
show me your code |
| 00:54 |
|
Emos |
http://pastebin.com/d4dec7700 |
| 00:54 |
|
Emos |
I cannot install DBD |
| 00:54 |
|
Emos |
the code is copied and pasted directly from http://github.com/jhannah/sand[…]/master/emos/x.pl |
| 00:54 |
|
deafferret |
do you have MySQL installed on your computer? |
| 00:55 |
|
deafferret |
x.pl should have nothing to do with MySQL |
| 00:56 |
|
deafferret |
when you run x.pl it bitches about DBD::mysql? |
| 00:57 |
|
Emos |
maybe I just pasted the wrong code of the sandbox |
| 00:58 |
|
Emos |
no |
| 00:58 |
|
Emos |
it asks me DBD |
| 00:58 |
|
Emos |
I don't know why |
| 00:59 |
|
deafferret |
well, Bio::EnsEMBL::Registry is truly evil if it's requiring MySQL for no reason. |
| 01:00 |
|
deafferret |
perl -MCPAN -e shell force install DBD::mysql |
| 01:02 |
|
Emos |
Failed during this command: |
| 01:02 |
|
Emos |
CAPTTOFU/DBD-mysql-4.012.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512 |
| 01:02 |
|
deafferret |
wget http://search.cpan.org/CPAN/au[…]ysql-4.012.tar.gz |
| 01:03 |
|
deafferret |
tar xvzf DBD-mysql-4.012.tar.gz |
| 01:03 |
|
deafferret |
cd DBD-mysql-4.012 |
| 01:03 |
|
deafferret |
perl Makefile.PL |
| 01:03 |
|
deafferret |
make |
| 01:03 |
|
deafferret |
make install |
| 01:03 |
|
deafferret |
(might not work) |
| 01:03 |
|
* deafferret |
shakes his fist at Bio::EnsEMBL::Registry |
| 01:04 |
|
Emos |
in which folder do i have to do that? |
| 01:04 |
|
deafferret |
src |
| 01:04 |
|
Emos |
can I use fink? |
| 01:04 |
|
deafferret |
dunno |
| 01:04 |
|
deafferret |
DBD::mysql won't REALLY install unless you install MySQL itself |
| 01:04 |
|
deafferret |
so if you want to install MySQL, feel free |
| 01:04 |
|
deafferret |
then DBD::mysql might actually work |
| 01:05 |
|
deafferret |
but you don't need it to WORK, you just need Bio::EnsEMBL::Registry to think it is |
| 01:05 |
|
* deafferret |
shakes his fist at Bio::EnsEMBL::Registry |
| 01:06 |
|
deafferret |
crap. next $work project is yuck |
| 01:06 |
|
Emos |
:-( |
| 01:07 |
|
Emos |
about what? |
| 01:07 |
|
deafferret |
https://ssl.omnihotels.com cookie problem :( bah |
| 01:08 |
|
Emos |
:-(:-( |
| 01:08 |
|
deafferret |
$day; $dollar++; |
| 01:08 |
|
deafferret |
$day++; $dollar++; |
| 01:08 |
|
deafferret |
$older++; $debt++; :) |
| 01:09 |
|
* deafferret |
owes his soul to the company store |
| 01:09 |
|
* deafferret |
loads 16 tons |
| 01:45 |
|
Emos |
I installed mysql qith fink |
| 01:46 |
|
Emos |
but DBD won't install |
| 01:46 |
|
Emos |
:-( |
| 01:46 |
|
Emos |
very sad |
| 01:46 |
|
Emos |
can't use your perfect script |
| 01:46 |
|
Emos |
Cannot find the file 'mysql_config' |
| 01:46 |
|
Emos |
that's the problem |
| 01:47 |
|
deafferret |
did you try DBD-mysql-4.012.tar.gz ? |
| 01:47 |
|
Emos |
yeah |
| 01:47 |
|
Emos |
the same |
| 01:47 |
|
Emos |
when i say make.pl |
| 01:47 |
|
Emos |
it gets stuck |
| 01:47 |
|
Emos |
Cannot find the file 'mysql_config' |
| 01:48 |
|
deafferret |
you meant 'make' right? |
| 01:48 |
|
Emos |
can't exec "mysql_config": No such file or directory at Makefile.PL line 82. |
| 01:48 |
|
Emos |
annot find the file 'mysql_config'! Your execution PATH doesn't seem |
| 01:48 |
|
Emos |
not contain the path to mysql_config. Resorting to guessed values! |
| 01:48 |
|
Emos |
Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. |
| 01:48 |
|
Emos |
Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located |
| 01:49 |
|
Emos |
Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. |
| 01:49 |
|
Emos |
Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located |
| 01:49 |
|
Emos |
Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. |
| 01:49 |
|
Emos |
Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located |
| 01:50 |
|
deafferret |
so when you searchlight (or whatever that thing in the upper right corner is called) for mysql_config there's no hits? |
| 01:50 |
|
deafferret |
http://www.nntp.perl.org/group[…]/09/msg10387.html |
| 01:51 |
|
Emos |
no |
| 01:54 |
|
deafferret |
does this install mysql_config? http://dev.mysql.com/downloads[…]1.html#macosx-dmg |
| 02:00 |
|
Emos |
http://search.cpan.org/dist/DB[…]mysql/INSTALL.pod |
| 02:01 |
|
Emos |
there's a way of installing it without mysql_config |
| 02:01 |
|
Emos |
but i don't understand how |
| 02:06 |
|
deafferret |
dunno. DBD::mysql installs fine on Linux. I've never tried on OS X |
| 02:06 |
|
deafferret |
no Mac here |
| 02:09 |
|
Emos |
is there a command |
| 02:09 |
|
Emos |
to search for a file |
| 02:09 |
|
Emos |
with commandline? |
| 02:09 |
|
deafferret |
find |
| 02:10 |
|
Emos |
i typed find mysql_config |
| 02:10 |
|
Emos |
it tells me no such file or directory |
| 02:10 |
|
Emos |
without searching |
| 02:10 |
|
deafferret |
find / -name "mysql_config" |
| 02:11 |
|
deafferret |
that's the same this searchlight does, only searchlight is faster (indexed) |
| 02:12 |
|
Emos |
but i think spotlight skips system files |
| 02:14 |
|
deafferret |
oh? perhaps |
| 02:15 |
|
Emos |
found |
| 02:15 |
|
Emos |
how can i feed it to the isntaller script? |
| 02:15 |
|
deafferret |
put it in your $PATH |
| 02:15 |
|
Emos |
?? |
| 02:15 |
|
deafferret |
same problem as $PERL5LIB |
| 02:15 |
|
deafferret |
echo $PATH |
| 02:16 |
|
Emos |
it doesnt paste here |
| 02:16 |
|
Emos |
but is "/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin" |
| 02:16 |
|
Emos |
ok |
| 02:17 |
|
Emos |
how can i put it in $path? |
| 02:19 |
|
deafferret |
if you can't figure out how to change your environment variables, then copy the program into one of those directories |
| 02:20 |
|
Emos |
wait |
| 02:20 |
|
Emos |
maybe i did it |
| 02:20 |
|
Emos |
WE did it |
| 02:21 |
|
Emos |
macos:perl EmanueleO$ perl prova3 |
| 02:21 |
|
Emos |
54806 chr6 39674566..40088359 |
| 02:21 |
|
Emos |
27185 chr1 25180339..25794796 |
| 02:21 |
|
Emos |
1815 chr11 477304..680702 |
| 02:21 |
|
Emos |
280730 chr18 316898..520907 |
| 02:21 |
|
deafferret |
woot! |
| 02:21 |
|
Emos |
581 chr19 21626334..21833272 |
| 02:21 |
|
Emos |
macos:perl EmanueleO$ |
| 02:21 |
|
Emos |
YUHOOOOO |
| 02:22 |
|
deafferret |
out.fasta should be sitting there |
| 02:25 |
|
Emos |
YES!!!! |
| 05:20 |
|
rbuels |
deafferret: you have saint-like patience. |
| 05:21 |
|
deafferret |
rbuels: I agree. I am awesome. |
| 05:22 |
|
rbuels |
i could not do what you did with Emos. |
| 05:22 |
|
rbuels |
start to end, that was 9 hours. |
| 05:22 |
|
deafferret |
he got me on a roll. If nothing else, I have momentum. :) |
| 05:22 |
|
rbuels |
9. |
| 05:22 |
|
rbuels |
hours. |
| 05:22 |
|
deafferret |
ya. burned 2 hours of no pay on that. -shrug- |
| 05:23 |
|
deafferret |
but now I've done my first Ensembl API, so thats cool |
| 05:24 |
|
rbuels |
true, you did at least get some knowledge out of it |
| 05:24 |
|
rbuels |
where is that guy at? he owes you like 20 beers and the indentured servitude of his firstborn |
| 05:25 |
|
* rbuels |
looks at the backscroll |
| 05:27 |
|
deafferret |
uci.edu |
| 05:28 |
|
rbuels |
ah thanks, i had only gotten through about 2 hours of it up to then |
| 05:28 |
|
rbuels |
lol |
| 05:28 |
|
deafferret |
21:35 -!- Emos [n=chatzilldhcp-077c-201.bic.uci.edu] has quit |
| 05:28 |
|
rbuels |
ah, there. |
| 05:28 |
|
rbuels |
well at least he's burning the midnight oil |
| 05:28 |
|
rbuels |
he'd better get himself a camel book |
| 05:29 |
|
deafferret |
i'm glad to give back one millionth of the open source I've received :) |
| 05:29 |
|
rbuels |
so how many extra modules did he have to install there... |
| 05:29 |
|
* rbuels |
greps for cpan |
| 05:30 |
|
rbuels |
Bio::ASN1::Garbage and DBD::mysql i think |
| 05:30 |
|
rbuels |
you know what's funny? |
| 05:30 |
|
rbuels |
there's actually a CXGN::Garbage namespace in our ball of mud |
| 05:32 |
|
rbuels |
what. the. |
| 05:32 |
|
rbuels |
google chrome os |
| 05:32 |
|
rbuels |
http://www.nytimes.com/2009/07[…]es/08operate.html |
| 05:33 |
|
deafferret |
sorry, my brain's done for today. 00:33 here |
| 05:33 |
|
rbuels |
heh OK |
| 05:33 |
|
deafferret |
watching The Wire, then bed :) |
| 05:33 |
|
rbuels |
night |
| 05:37 |
|
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| 06:39 |
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| 07:47 |
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| 11:51 |
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