Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-24

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13:13 kblin hey folks, Bio::SeqFeature::Generic mentions a Bio::SeqFeature::Gene class, I can't find a Gene.pm in Bio/SeqFeature/ though.. what am I missing?
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15:50 deafferret kblin: the Gene/ subdirectory has a bunch of stuff. I don't like the way that POD is worded... maybe it should mention "the ::Gene::* namespace" or something
15:58 kblin ah, I see
15:59 kblin thanks
16:28 pyrimidine joined #bioperl
16:30 flu_ new BLAST out ftp://ftp.ncbi.nlm.nih.gov/blast/e​xecutables/blast+/LATEST/ChangeLog
16:31 pyrimidine flu_: already notified the bp list about it
16:31 pyrimidine pretty interesting addition, the BLAST archive format
16:32 flu_ that is what caught my eye as well
16:32 pyrimidine yeah, wondering if there is a way to abuse that for alignment storage, ala SAM/BAM
16:32 pyrimidine but allowing protein sequences
16:34 flu_ interesting, hadn't thought about that.  I was excited by the fact that I wouldn't have to re-run blast jobs when a user requested a different format or maintain reformatting scripts.
16:35 pyrimidine well, that too :)
17:09 dbolser how do I create a regular expression from a bunch of strings?
17:11 pyrimidine dbolser: qr/$foo/
17:11 dbolser does qr/$foo$bar$baz/ work?
17:11 pyrimidine should
17:11 pyrimidine it'll concatenate them (not alternation)
17:12 dbolser does qr/$foo\s$bar\s$baz/ work?
17:12 dbolser right
17:12 pyrimidine there is this nugget in LocatableSeq: $string =~ s{[$GAP_SYMBOLS$FRAMESHIFT_SYMBOLS]+}{}g;
17:13 pyrimidine dbolser: yes, that should work
17:13 dbolser cool
17:13 dbolser what is that trailing {}g doing?
17:14 dbolser oh I see
17:14 dbolser s{}{}
17:14 pyrimidine global match and replace
17:14 dbolser confused because it wasn't s///
17:14 pyrimidine you can use m/$foo/g to match everything
17:14 deafferret frameshift symbols? yikes
17:14 pyrimidine yep
17:15 pyrimidine unfortunately have to build that into the class's coord logic
17:16 deafferret dear lord.... where do frameshift symbols occur in the actual universe?
17:16 pyrimidine FASTA
17:16 deafferret in genbank/ensembl somewhere?
17:16 pyrimidine Or. I should qualify that, the Fasta set of programs
17:16 deafferret ffs. I've never heard of that
17:16 pyrimidine tfastx/y
17:17 dbolser deafferret: you've never heard of fasta?!?!?
17:17 * dbolser swoons
17:17 * deafferret curses some more, upping his civility quotient
17:17 deafferret dbolser: i've never hear of frameshift symbols
17:17 deafferret heard
17:17 dbolser cheers pyrimidine my regexp is working nicely
17:17 dbolser deafferret: oh
17:17 dbolser sorry
17:18 pyrimidine good! :)
17:19 pyrimidine deafferret: http://github.com/bioperl/bioperl-li​ve/blob/master/t/data/5X_1895.FASTXY
17:20 pyrimidine The first hit has '/' and '\' in the alignment
17:20 pyrimidine those are frameshifts
17:21 deafferret wut the frack? as in "skip a single base at this point" ?
17:21 pyrimidine yep
17:21 deafferret this is news to me
17:22 pyrimidine or 'shift one base forward/back'
17:23 pyrimidine and, since the coords are based on the nucleotide sequence, even trickier to keep track of
17:23 deafferret so we're still reading 3 bases at a time as a codon... but there are blips in the RNA where we skip a base during translation?
17:23 pyrimidine yes
17:24 deafferret god: stop being a jerk. that's just not cool. this biology crap was hard enough already
17:27 pyrimidine :)
17:27 deafferret 90% of the google hits I'm finding are just talking about "use frame 1 not frame 2"   http://en.wikipedia.org/wiki/Frameshift
17:27 deafferret what you're saying is "use frame 1 until you get to base 30 then use frame 2"  -- or am I drunk?
17:27 pyrimidine yes
17:27 deafferret oh good. i am drunk.
17:27 deafferret good to know.
17:28 deafferret is there a paper on this I can run around UNO and freak out with?
17:29 pyrimidine of course not, that would be too easy :)
17:29 deafferret so... the only evidence I have so far is a '/' character in 5X_1895.FASTXY   :)
17:29 deafferret am I on canded camera?
17:29 deafferret candid?
17:29 pyrimidine there might be something in the Fasta docs on this
17:30 deafferret is this "screw with Jay's head" day?
17:30 pyrimidine but good luck finding it
17:30 pyrimidine So, the problem we face with the current alignment system in BioPerl is we have one class that has to deal with all the differences
17:30 pyrimidine simple sequences
17:30 pyrimidine translated sequences
17:30 pyrimidine reverse-translated seqs
17:31 pyrimidine and the differences in coordinates between them all
17:31 pyrimidine not to mention the various different symbols (gaps, residues, frameshifts)
17:31 pyrimidine so, yes, it's a fucking nightmare, to put it mildly
17:34 deafferret um... there isn't even a term for this nightmare?  usually  (Google) when people say "frameshift" they just mean "frame 2 instead of frame 1"
17:35 deafferret i'm finding no references to "change your frame when you hit base 30"
17:35 deafferret and entrez is down
17:35 pyrimidine there are three possible frames of translation for a protein
17:35 deafferret .entrez 5X_1895
17:35 deafferret EBOTFAIL
17:36 pyrimidine oh, I wouldn't use that
17:36 pyrimidine it's just the example file for bioperl test purposes for a Fasta run
17:36 deafferret i want any real-world example
17:36 dnewkirk In biology?
17:37 deafferret ya. any CDS which says "skip a base here"
17:37 deafferret does  // mean "skip two bases forward" ?
17:38 dnewkirk http://www.ncbi.nlm.nih.gov/pubmed/20507907
17:40 dnewkirk It's more common than is currently realized I'd imagine.
17:40 deafferret oh... wow. nih.gov is blocked from this workstation (wired) but available from my laptop (wireless)
17:40 deafferret corporate IT is getting weirder
17:40 perl_splut wireless is probably in the DMZ for the network, heheh
17:41 deafferret dnewkirk++ # holy crap. thank you.
17:42 deafferret i was the last one to know about this?  -nervous laugh-
17:42 pyrimidine Just to screw with you more, you can also have programmed frameshifts during translation
17:43 deafferret what does that mean?
17:43 pyrimidine http://arjournals.annualreviews.org/d​oi/abs/10.1146/annurev.genet.30.1.507
17:44 pyrimidine (I like the translational hop myself)
17:45 deafferret is there a genbank ID associated with pubmed 20507907 ? I can't see the full article from here ($work[0])
17:46 deafferret 1996 ?? wow. I am less educated then I thought
17:48 dnewkirk It was something my profs (briefly) mentioned in a grad course this last quarter, but a couple of them are translation folks. It's not something commonly addressed...
17:51 pyrimidine http://www.ncbi.nlm.nih.gov/nuccore/DQ846750.1
17:51 pyrimidine deafferret: ^^
17:51 pyrimidine in the feature table, there is an example note
17:52 pyrimidine these are more common in viruses
17:53 * pyrimidine is glad to add to deafferret's reading list
17:55 * deafferret fails to understand "ORF1b; translated from ORF1a by programmed -1 ribosomal frameshift"
17:55 deafferret ORF1 is a single translation that skips 7 bases in the middle?
17:56 pyrimidine screwy, ain't it?
17:56 deafferret 225..9751 ?
17:56 deafferret is that what that says?
17:57 pyrimidine yes, essentially
17:58 pyrimidine or there could be some uncertainty about the frame for that region
17:58 * pyrimidine is curious how GFF3 handles that....
17:58 deafferret so...    ...VEAVNQ///////LRAPHIF...   ?
17:58 deafferret or would that be considered 2 exons with a single / ?
17:58 pyrimidine in this case, it looks likek they describe it as two CDS
17:59 pyrimidine *like
17:59 pyrimidine so, like two exons here
17:59 deafferret w o w
18:00 * deafferret goes back to brain dead corporate survey software
18:01 pyrimidine ...and that was your genomics lesson for today.  Please tune in to #bioperl for more complete oddities in the field that are a PITA to work with!
18:01 * pyrimidine also goes back to work
18:02 deafferret :)
18:03 deafferret i love how half of bio* learning is   "you know how you thought that you knew how something worked? are you sitting down?"
18:03 dnewkirk It's the giant asterisk next to every statement :).
18:05 pyrimidine yes, that's what frustrates the physicists and engineers here who like things to be very precise
18:05 pyrimidine they don't like exceptions to the rule
18:06 pyrimidine biology is all about exceptions to the rule
18:06 deafferret "hold on loosely, but don't let go"    ... it's very zen
18:11 CIA-95 Bio-FeatureIO: Chris Fields master * rf17eba9 / t/data/hg19_sample.bed : add new bed example; old one is shite - http://bit.ly/beKNSw
18:12 deafferret lol
18:12 pyrimidine Here is the old version:
18:12 pyrimidine chr1010test-coordinates-1
18:12 pyrimidine (that's it)
18:12 deafferret i'm not up to speed on .bed files
18:13 pyrimidine http://genome.ucsc.edu/FAQ/FAQformat#format1
18:14 dnewkirk chr start end undef undef strand
18:14 dnewkirk pretty much all I ever use anyway :)
18:15 deafferret ah. .gff minus my hatred of tabs?
18:15 dnewkirk it's tab delimited
18:15 * deafferret sighs
18:16 pyrimidine I think you're supposed to be able to split on any whitespace
18:16 dnewkirk using anything else would be suicide with what some people shove in bed files.
18:16 pyrimidine that's true
18:17 deafferret like tabs?   ;)
18:17 pyrimidine [\s\t]+
18:17 dnewkirk <- makes his .csv files tab delimited
18:18 deafferret pipes > tabs > .csv
18:47 genehack but greatest of them all is YAML
18:47 * genehack ducks and runs for cover
18:56 * deafferret likes YAML  :)
18:57 perl_splut \s contains \t in it
18:57 perl_splut so [\s\t] is any whitespace or any tab...
18:59 pyrimidine perl_splut: yes, that's true
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18:59 deafferret 在過去的七天內,我的付出得到了認可或嘉獎
19:00 newtobioperl I am trying to load my GFF file to mysql database using bp_seqfeature_load.pl but I got this error
19:00 newtobioperl [BioComplexity-5:/usr/local/bin] minh% perl bp_seqfeature_load.pl
19:00 pyrimidine Мне очень понравилась ваша фотография и письмо
19:01 newtobioperl nstall_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC
19:01 pyrimidine heh
19:01 deafferret cpan DBD::mysql
19:04 newtobioperl done!!!
19:04 newtobioperl I try to use perl bp_seqfeature_load.pl
19:04 newtobioperl get this error
19:04 newtobioperl DBI connect('test','',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) at /Library/Perl/5.8.6/Bio/DB/S​eqFeature/Store/DBI/mysql.pm line 212
19:05 newtobioperl -------------------- EXCEPTION --------------------
19:05 dnewkirk service mysqld start (if your on linux)
19:05 perl_splut do you have mysql installed and running on the mac?
19:05 newtobioperl i am Mac OSX
19:05 newtobioperl i installed it manually
19:05 newtobioperl how to check whether mysql is installed successfully?
19:06 deafferret "I really liked your picture and a letter"   laugh
19:06 deafferret this survey question, translated via google translate from chinese to english, is: "My department, a manager at least so to him / her to ask what the problem is pleasant"
19:07 deafferret would you say you strongly agree? somewhat agree? somewhat disagree? ....  :)
19:08 pyrimidine newtobioperl: which mysql
19:08 pyrimidine to see if it's in your PATH
19:08 newtobioperl mysql: Command not found
19:08 deafferret sudo apt-get install mysql-server
19:09 newtobioperl Reading Package Lists... Done
19:09 newtobioperl Building Dependency Tree... Done
19:09 newtobioperl E: Couldn't find package mysql-server
19:09 newtobioperl I am using Mac
19:09 deafferret sudo apt-cache search mysql
19:09 newtobioperl 10.4
19:10 newtobioperl dbi-pm586 - Perl Database Interface by Tim Bunce
19:10 newtobioperl libdbi-drivers-mysql - MySQL driver for libdbi
19:10 newtobioperl mysql - Open Source SQL database
19:10 newtobioperl mysql-client - Open Source SQL database - Client
19:10 newtobioperl mysql-dev - Open Source SQL database - Development headers and libraries
19:10 newtobioperl what package are we looking for?
19:10 deafferret sudo apt-get install mysql
19:12 newtobioperl ok
19:12 newtobioperl which mysql
19:12 newtobioperl test
19:12 newtobioperl when I type which mysql
19:13 newtobioperl got this: /sw/bin/mysql
19:13 newtobioperl (i have been using FInk)
19:13 deafferret 'which mysql' says /sw/bin/mysql but when you type 'mysql' you get 'not found'?
19:13 deafferret hash -r   ?
19:14 newtobioperl > mysql
19:14 newtobioperl > ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
19:14 deafferret /etc/init.d/mysql start    ?
19:15 newtobioperl csh: /etc/init.d/mysql: Command not found.
19:15 deafferret where do you usually go to start daemons?
19:15 deafferret /etc/init.d  ? /etc/rc.d   ?   some combination?
19:15 deafferret each OS puts those wherever
19:17 newtobioperl sudo /etc/rc.d
19:17 newtobioperl sudo: /etc/rc.d: command not found
19:17 deafferret these aren't commands. these are directories (maybe)
19:17 newtobioperl what do you mean start dawmons? I am sorry i am new to mac
19:17 pyrimidine I think Mac OS X has a start up script and a PrefPane switch
19:17 deafferret how do you restart apache?
19:17 deafferret MAC?? uh
19:17 newtobioperl Apache: Sytem References...
19:17 pyrimidine newtobioperl: how did you install mysql?
19:17 deafferret sorry, I assumed linux. i've never run daemons on mac
19:18 newtobioperl -->sharing
19:18 deafferret i think in control panel there's a mysql on/off switch?
19:18 deafferret don't remember
19:18 newtobioperl --> stop Personal web shareing
19:19 pyrimidine oh, you used fink
19:19 pyrimidine ok
19:19 newtobioperl well when I use sudo apt-get install mysql
19:20 pyrimidine you don't want that
19:20 newtobioperl it installed mysql to Fink folders
19:20 newtobioperl what can I do?
19:20 pyrimidine well, you have a couple of options
19:20 pyrimidine you can add /sw/bin to your PATH
19:21 pyrimidine or uninstall mysql via apt, and use the MySQL official bundle
19:21 newtobioperl my goal is to use bp_seqfeature_load
19:21 newtobioperl to load my GFF files to mysql
19:22 pyrimidine right, but you need a DB backend
19:22 newtobioperl yes
19:22 pyrimidine Pg, MySQL, SQLite, BDB, etc
19:22 newtobioperl How can I add /sw/bin to my PATH?
19:22 newtobioperl wait
19:22 newtobioperl i actually had that
19:23 newtobioperl in my PATH
19:23 pyrimidine try opening up a new shell
19:23 pyrimidine and recheck
19:23 newtobioperl recheck mysql?
19:23 newtobioperl > mysql
19:23 newtobioperl > ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
19:24 newtobioperl still
19:24 pyrimidine that means you haven't started the mysql server
19:24 newtobioperl i think I also installed Mysql manually because i see there is a mysql folder in usr/local
19:25 newtobioperl but its not in my PATH
19:26 pyrimidine do you have a startup item?
19:26 pyrimidine http://www.womenrussia.com/phrases.htm
19:27 pyrimidine oh, wait, that was for deafferret
19:27 pyrimidine http://www.jonmaddox.com/2007/10/27/start​-and-stop-mysql-in-mac-os-x-105-leopard/
19:27 pyrimidine :)
19:27 newtobioperl lol
19:27 newtobioperl i saw a woman and something in russian
19:27 newtobioperl hehe
19:27 pyrimidine best not to look too much, it's a creepy site
19:28 newtobioperl sudo: /Library/StartupItems/MySQLCOM/MySQLCOM: command not found
19:29 pyrimidine ok, so there is no startup script (that would be the equivalent of the /etc/init.d/mysql script deafferret mentioned above)
19:30 newtobioperl how can I install the startup script?
19:31 pyrimidine http://pdb.finkproject.org/pdb/package.ph​p/mysql?rel_id=10.6-x86_64-current-stable
19:31 pyrimidine use 'mysqld_safe --user=mysql &'
19:31 pyrimidine as root
19:31 pyrimidine sudo
19:32 pyrimidine newtobioperl: personally, I wouldn't go this route, though, for Mac.  You can normally get a .dmg from dev.mysql.org that works
19:33 newtobioperl oh I just open the mysql dmg package and see MYSQLStartupIteam
19:33 newtobioperl installed it
19:34 pyrimidine you may have to fidgit with the PATH to get it working from command line
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19:34 newtobioperl do I need to uninstall mysql from /sw/bin
19:34 brandi1 left #bioperl
19:34 newtobioperl ?
19:35 pyrimidine newtobioperl: you'll have two executables in your PATH, so yes
19:35 pyrimidine brb # free donuts
19:35 newtobioperl ok
19:36 newtobioperl lets me know when you are back
19:43 newtobioperl actually, after i follow this guide
19:43 newtobioperl http://gmod.org/wiki/GBrows​e_MacOSX_HOWTO#The_Fink_Way
19:43 newtobioperl it s working now
19:56 pyrimidine back
19:56 pyrimidine newtobioperl: good to hear
19:56 pyrimidine the key tough spot isn't MySQL, but DBD::mysql (and that is a lot easier than it used to be)
19:57 newtobioperl pyrimidine, what is the easy way to install phpmyadmin on mac
19:57 newtobioperl ?
19:57 newtobioperl so It means that i am fine with DBD::mysql?
19:57 pyrimidine well, it should (if you installed via fink)
19:58 newtobioperl because when I type perl bp_seqfeature_load.pl it doesnt give me any error
19:58 newtobioperl i tried to install phpmyadmin
19:58 pyrimidine that's promising
19:58 newtobioperl but
19:58 newtobioperl when i go to locahost/phpmyadmin, it shows me the whole folders
19:58 newtobioperl and files
19:58 newtobioperl instead of phpmyadmin GUI
19:59 pyrimidine I use MySQL Workbench
19:59 newtobioperl does it mean that i dont have PHP?
19:59 pyrimidine not sure
19:59 pyrimidine I stay as far away from PHP as possible
20:00 pyrimidine (well not really :)
20:00 newtobioperl lol
20:00 pyrimidine but I don't use phpmyadmin, so can't help you
20:00 newtobioperl i just want to create a database and load my gff file in there
20:01 newtobioperl when I login to mysql, and use create database, it gives me the "permission" error
20:01 newtobioperl ERROR 1044 (42000): Access denied for user ''@'localhost' to database 'hiv_0815'
20:07 pyrimidine need a password?
20:09 perl_splut note the lack of a username in front of the @
20:09 newtobioperl i just downloaded mysql workbench
20:09 newtobioperl and installed it
20:10 newtobioperl but when I click on MYSQLWorkBench, i dont see anything
20:10 perl_splut http://www.materialstoday.com/view/11790​/materials-today-2010-cover-competition/
20:11 newtobioperl is that for me?
20:18 newtobioperl left #bioperl
20:33 * dnewkirk thinks whoever designed the palletes in RColorBrewer was dropping acid
20:36 dnewkirk anyone know how to get the standard red/black/green for typical microarray heatmaps?
20:46 dnewkirk nevermind
20:51 bag_ joined #bioperl
21:46 * deafferret uses phpmyadmin
21:48 pyrimidine deafferret like russian wives
21:50 deafferret my best friend's wife is from Tajikistan
21:50 deafferret close enuf
22:01 pyrimidine left #bioperl
22:02 CIA-95 Bio-FeatureIO: Chris Fields master * rb7d4100 / (lib/Bio/FeatureIO/bed.pm t/bed.t): a bit further with bed format, but still borken - http://bit.ly/bCJcqF
22:56 bag_ left #bioperl
23:13 ank left #bioperl

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