Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-07

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Time Nick Message
01:56 alper joined #bioperl
12:20 alper joined #bioperl
14:22 ericlee joined #bioperl
14:22 ericlee anyone here  could help me with my bio script?
15:11 deafferret perhaps. what's your question?
15:34 perl_splut faster to just ask the question and wait for answers, heheh
15:44 deafferret "don't ask to ask, just ask. those who ask to ask risk axing"
15:46 perl_splut hahah
16:08 ericlee anyone here?
16:09 ericlee http://erxz.com/pb/18613
16:09 ericlee My script here. And it could get the sequences in list one by one from a file.
16:10 ericlee But it seems that this script cannot work very well, could you tell me how to fix that?
16:11 ericlee hi?
16:14 deafferret hola
16:14 ericlee hi, thanks. Have you viewed my script?
16:15 ericlee Actually I don't know what's wrong in my script. :(
16:16 sphere8 joined #bioperl
16:16 deafferret ericlee: so what are you getting when you run it?
16:16 sphere8 left #bioperl
16:16 deafferret and what were you expecting?
16:17 ericlee it shoud get the sequences which tags at a list file.
16:18 deafferret so what are you getting when you run it?
16:18 ericlee I will paste a result.
16:20 ericlee http://erxz.com/pb/18615
16:21 ericlee LIST is the list file holds the tags, SEQ is the sequences file, RUN is the result, you will find that was very odd.
16:21 deafferret what's odd about it? reduce to a single sequence so it's more obvious
16:22 ericlee don't you find errors here?
16:22 ericlee The result is the SEQ itself.
16:22 deafferret it's easier to help you with less data, unless I need all this data to see the problem
16:23 ericlee Okay, I tell you what I mean.
16:23 deafferret so what did you want the first line of __RUN__ to look like?
16:23 ericlee The output is totally the sequences file I provide.
16:24 ericlee Do you read my script?
16:24 deafferret yup
16:24 ericlee SEQ == RUN
16:25 deafferret the so what did you want the first line of __RUN__ to look like?
16:25 ericlee if the tag from the list exists at the sequences file just output the sequence.
16:25 ericlee If not, output nothing.
16:28 ericlee clear? I don't know why it will repeat that because at my script I have set up the test condition to see whether the tag from list is equal to the tag at the sequences file.
16:28 ericlee any idea?
16:28 deafferret you want the sequence and not the ID?
16:29 ericlee sorry, do you understand the meaning of ">$id\n$raw_seq\n"?
16:29 deafferret yes. I'm wondering if you do. You said "just output the sequence", but obviously that outputs the ID and the sequence
16:29 deafferret right?
16:29 ericlee yes, seq and ids.
16:30 deafferret oh, ok. so you like the format, but were expecting fewer matches in __RUN__  ?
16:30 ericlee right.
16:31 deafferret so you're expecting 9 lines of __RUN__ instead of 50?
16:32 ericlee if matches. just output the result.
16:32 ericlee just one time.
16:32 deafferret so you're expecting 9 lines of __RUN__ instead of 50?
16:33 ericlee if all of 9 lines at LIST will match 9 sequences at SEQ, yes.
16:34 deafferret ok. now I understand the question.  :)
16:34 ericlee are u a devloper at bp?
16:35 deafferret this is me:  http://www.bioperl.org/wiki/User:Jhannah
16:36 ericlee do you know how to fix my script?
16:36 deafferret sure. I'm setting it up on github for you do download
16:36 deafferret once it's working
16:36 ericlee what's wrong at my script?
16:36 deafferret I don't know yet. I'm setting it up on my server so I can debug it
16:38 ericlee how is going?
16:39 ericlee I guess you could read my script then find out what's going on.
16:39 ericlee because my script is easy to read.,
16:39 deafferret you've got 15 things going on. I need to run it to figure out what's wrong. unless you don't want my help.  :)
16:40 deafferret patience, grasshopper
16:40 ericlee clear.
16:41 deafferret http://github.com/jhannah/s​andbox/tree/master/ericlee
16:43 ericlee sorry, what's that?
16:44 deafferret that's where I set up your code so people other than you (me) and debug it for you
16:45 ericlee thanks, it's 12:45 am now.
16:46 ericlee what's your idea about the situation?
16:47 deafferret if ($item =~ /$id/i)     $id is being used as a regex
16:47 deafferret so you need to escape $id        if ($item =~ /\Q$id\E/i)
16:47 deafferret (not yet proven)
16:47 deafferret result set is now 0. is that expected?
16:48 ericlee huh, yes
16:49 deafferret yup. that was it. fixed, demo:  http://github.com/jhannah/s​andbox/tree/master/ericlee
16:50 deafferret i cheated one of the seq.fasta sequences into the list.txt, and poof! it shows up, but nothing else does
16:50 ericlee that means works well.
16:51 deafferret do you understand what the problem was and the resolution?
16:52 ericlee \Q is the key, it will tell the string is the normal string. not a regex.
16:52 ericlee I encountered  a problem before.
16:52 ericlee like use \Q
16:53 deafferret yup. perldoc perlre
16:57 ericlee thanks very much.
16:57 ericlee :)
16:58 deafferret :)  you're welcome.  enjoy
17:01 ericlee see ya~
17:02 deafferret toodles
17:57 Emos joined #bioperl
17:57 Emos hello there!
17:57 Emos is anyone online?
17:57 * deafferret waves
17:58 Emos hi
17:58 Emos I'm new to perl
17:58 Emos i'm a biologist
17:58 Emos I just installed bioperl
17:58 deafferret welcome!  :)  http://bioperl.org/wiki/IRC
17:59 Emos thanks a lot
17:59 Emos first of all, I would like to know if you can suggest me some reading
17:59 Emos apart from tutorials in bioperl.org
17:59 Emos like a book
17:59 Emos that can introduce me directly to bioperl
18:00 Emos and then I was trying to use a script that downloaded some sequences from refseq and made a fasta file for me
18:00 Emos bet it gives me an error
18:01 deafferret http://books.google.com/books?id=OG2xVZnf_ckC&am​p;dq=beginning+bioperl&source=gbs_navlinks_s
18:01 deafferret what error? nopaste your code and results:  http://sial.org/pbot/
18:02 Emos macos:perl EmanueleO$ Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.8.8​/darwin-thread-multi-2level /Library/Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/​darwin-thread-multi-2level /System/Library/Perl/5.8.8...
18:02 Emos .../Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8​/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.​8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at getgenomseq line 7.
18:02 Emos > BEGIN failed--compilation aborted at getgenomseq line 7.
18:03 deafferret don't paste in channel. paste here:  http://sial.org/pbot/
18:03 deafferret how did you install BioPerl?
18:03 Emos cpan
18:05 deafferret have you installed the "Ensembl API" ?  http://bioperl.org/wiki/HOWTO:Getting_Genom​ic_Sequences#Using_the_Perl_API_at_ENSEMBL
18:06 deafferret (I have not done this, so I might not know what I'm talking about.)
18:06 Emos no i havent
18:06 Emos but I am not able to
18:06 deafferret It appears that Bio::EnsEMBL::Registry is not part of BioPerl. It's a part of the Ensembl API
18:08 deafferret Is there some reason you're not just using Bio::Perl get_sequence() ?
18:08 Emos AH
18:08 deafferret http://search.cpan.org/~cjfields/Bio​Perl-1.6.0/Bio/Perl.pm#get_sequence
18:09 Emos is it possible to get sequences and create a multifasta file for them?
18:11 deafferret sure. get_sequence() plus a Bio::SeqIO object
18:13 deafferret give me 3 refseq IDs you want
18:13 deafferret is "multifasta" the same thing as "fasta" ?
18:14 Emos DISC1, ACE, ACTC
18:14 Emos for example
18:14 Emos I would like to automate a script
18:14 Emos that gets 100k bases before, after, and all the sequences of these genes
18:15 deafferret um. that's several problems. lets start with the first one  :)
18:15 Emos for example 100kb before - GENE - 100kb after
18:15 Emos :-)
18:15 deafferret MSG: acc DISC1 does not exist
18:17 deafferret http://github.com/jhannah/sandbox/tree/master/emos
18:19 Emos yes, the problem could be that the gene symbols are not unambiguous
18:20 Emos maybe, if I need also 100kb before and after each gene, I have to convert gene symbols in genomic coordinates
18:20 Emos then add 100k
18:20 Emos do you think it's possible
18:20 Emos ?
18:20 deafferret I don't know refseq, sorry. anything's possible in BioPerl.  :)
18:21 deafferret step 1: if you want to fetch whatever "DISC1" is, you'll need to find and use a unique ID for that
18:22 Emos http://www.genecards.org/cgi​-bin/carddisp.pl?gene=disc1
18:25 Emos I have a general quesiton
18:26 Emos if I'm searching, for example, for a script that does something (in this case: that gets genomic coordinates for a gene), where do I search?
18:27 Emos http://doc.bioperl.org/releases/bioperl-1.6.0/
18:27 Emos here
18:27 deafferret bioperl.org, google.com
18:27 Emos there is no search box
18:27 deafferret search.cpan.org
18:27 rbuels Emos: usually people don't publish little scripts like that though
18:27 rbuels Emos: maybe you can make a site called "Emos Script Archive"
18:27 deafferret rbuels: tag! you're it!
18:27 * deafferret runs
18:27 rbuels shit
18:28 deafferret github.com/emos
18:28 Emos doesn't exist
18:28 Emos what is it?
18:28 deafferret that's where you're going to put all your awesome code  :)
18:28 deafferret create an account.  :)
18:30 Emos :-)
18:36 Emos is this ok?
18:36 Emos http://doc.bioperl.org/releases/bioper​l-1.6.0/Bio/Coordinate/GeneMapper.html
18:47 deafferret ok? what do you mean?
18:52 deafferret rbuels++ svn update pulls t/bugzilla !!!
18:52 deafferret rbuels IS DA MAN!!
18:55 deafferret Emos: I can't get get_sequence() to fetch any of these IDs  http://www.genecards.org/cgi​-bin/carddisp.pl?gene=disc1
18:55 deafferret there are other ways, I assume
18:56 Emos I'm trying to get genomic coordinates of a gene
18:57 Emos http://bio.perl.org/wiki/HOWTO:Gettin​g_Genomic_Sequences#Using_Bio::DB::En​trezGene_to_get_genomic_coordinates
18:57 Emos but that script there I cannot understand
18:57 Emos how can I tell him the gene I'm interested in
18:58 deafferret $id = 'DISC1';
18:58 deafferret or script.pl DISC1
18:58 deafferret 'shift' pulls the first command-line argument
18:59 Emos Global symbol "$id" requires explicit package name at getcoord line 4.
18:59 Emos Execution of getcoord aborted due to compilation errors.
19:00 deafferret my $id = 'DISC1';
19:00 Emos oh why with my?
19:01 * rbuels gulps
19:01 Emos it doesn't work anyway
19:01 Emos it tells ms: ID?
19:02 deafferret perldoc perlintro "variable scoping"
19:02 deafferret remove this line    my $id = shift or die "Id?\n"; # use a Gene id
19:02 deafferret are you on linux?
19:03 deafferret or OS X?
19:06 Emos OSX
19:06 Emos it gives me a longer error
19:06 Emos MSG: Failed to load module Bio::SeqIO::entrezgene. .....
19:12 deafferret paste the full error here:  http://sial.org/pbot/
19:12 Emos this url tells me 404 not found
19:15 deafferret lol
19:15 deafferret oops
19:16 deafferret sorry
19:17 deafferret http://pastebin.com/ for now I guess
19:18 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient. Ask your question and wait. Paste to http://pastebin.com/ (http://sial.org/pbot/ is down)
19:18 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient. Ask your question and wait. Paste to http://sial.org/pbot/
19:18 deafferret ChanServ: you suck
19:19 deafferret Freenode--
19:20 Emos posted there
19:20 Emos pastebin.com
19:20 rbuels Emos: you need to give the url to the thing you pasted
19:21 Emos http://pastebin.com/d6cb555c3
19:21 Emos sorry I'm a disaster
19:22 rbuels Emos: which version of bioperl is this
19:22 Emos 588
19:23 deafferret wow!!  ;)
19:23 Emos builtin in osx
19:23 * rbuels smacks deafferret
19:23 Emos is it right?
19:23 * deafferret puts his shock collar back on
19:23 rbuels i'm looking into it
19:23 deafferret where oh where is/was  Bio::ASN1::EntrezGene ??
19:24 Emos sorry
19:24 * rbuels smells a bug
19:24 deafferret yikes... 2005...?  http://search.cpan.org/~mingyi​liu/Bio-ASN1-EntrezGene-1.091/
19:25 rbuels ah, it's external....
19:25 deafferret Emos: can you nopaste whatever source code you ran, followed by that error?
19:25 Emos is it a problem of script not installed?
19:25 rbuels oh.
19:25 rbuels 'Bio::ASN1::EntrezGene'     => '0/parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]',
19:25 rbuels in recommends of Build.PL
19:26 Emos http://pastebin.com/d71d34e59
19:26 rbuels Emos:  you need to use CPAN to install the Bio::ASN1::EntrezGene module
19:27 Emos what is the command in CPAN?
19:27 deafferret e.g.   cpan install Bio::ASN1::EntrezGene
19:27 rbuels at the cpan> prompt, you would type 'install Bio::ASN1::EntrezGene'
19:28 * rbuels is not pleased about this 'recommended modules' business
19:28 * rbuels feels a rant coming on
19:29 Emos is there a general way to know which modules are installed in my pc and which arend't?
19:29 rbuels you can look for the file, like 'locate EntrezGene.pm'
19:30 rbuels or you can sometimes do 'perdoc perllocal'
19:30 Emos thanks, it works now!!!
19:30 rbuels which usually lists all the things you've installed with cpan
19:30 rbuels Emos: congrats
19:31 rbuels deafferret: this is a systemic problem.  parts of bioperl have dependencies on things that really have nothing to do with other parts
19:31 rbuels deafferret: and it has been pushed under the rug by just saying they are 'recommended'
19:31 deafferret sounds swampy
19:44 Emos do you think it is possible to use this script
19:44 Emos http://bio.perl.org/wiki/HOWTO:Getting​_Genomic_Sequences#Using_Bio::DB::GenB​ank_when_you_have_genomic_coordinates
19:44 Emos to get the sequence of the coordinates I just got with the other script?
19:47 deafferret yes? isn't that the point of that wiki page?
19:49 Emos yes
19:49 Emos but then it tells me to start from RNAfactory
19:50 Emos how can I use the output of the previous script as imput of this one?
19:51 deafferret in script2.pl:  while (<>) { # do something with STDIN }
19:54 Emos didn't understand
19:56 Emos I'm trying to do something like this
19:56 Emos http://pastebin.com/d6926a06d
19:59 deafferret what is the output of the previous script?
20:02 Emos http://pastebin.com/d76d65672
20:02 Emos because I just cut and paste parts of the 2 scripts
20:03 Emos but I didn't tell the second to use teh output of the first
20:05 deafferret my ($id, $start, $stop) = split /\s+/, <>;
20:06 rbuels deafferret: is that going to work?  what context is <> in there
20:06 deafferret NT_025741.153977456639988359
20:06 deafferret whoah... that pasted weird
20:06 deafferret NT_025741.15 39774566 39988359
20:07 Emos so I just have to write
20:07 Emos my ($id, $start, $stop) = split /\s+/, <>;
20:07 Emos ?
20:07 Emos what does this do?
20:07 deafferret then use those vars wherever in script 2
20:07 deafferret <> says "take the first line of STDIN"
20:07 Emos ah ok
20:08 deafferret then    chomp $stop;   probably
20:08 deafferret to get rid of newline char
20:26 Emos http://pastebin.com/d5cb99f43
20:26 Emos I am at this point
20:27 Emos the program runs
20:27 Emos but gets stuck
20:28 deafferret gets stuck where? what output do you get?
20:28 Emos output
20:28 Emos NT_025741.153977456639988359
20:28 Emos and then the cursor blinks
20:28 Emos but doesn't do anything more
20:29 deafferret are you trying to pipe one program into another? paste what you're trying to run
20:29 Emos http://pastebin.com/d5cb99f43
20:29 deafferret are you typing    script1.pl | script2.pl   ?
20:30 Emos no, they are in the same file
20:30 Emos i just run the file
20:30 Emos perl file
20:30 Emos perl file.pl
20:30 deafferret oh. I thought you were trying to pass the STDOUT of script1 into script2
20:30 Emos I don't know what you mean
20:31 deafferret :)
20:31 Emos :-(
20:31 Emos I'm too ignorant
20:31 Emos tomorrow I'll buty the book you suggested me
20:32 deafferret i'll rework it for you
20:32 Emos thanks!
20:33 Emos what do you do in your life? are you a bioinformatician?
20:33 pingou (if yes, where ? :))
20:34 deafferret http://www.bioperl.org/wiki/User:Jhannah
20:37 deafferret installing deps
20:38 deafferret wow... did this mess just re-install BioPerl?
20:40 Emos ???
20:41 deafferret -laugh- ick Bio::ASN1::EntrezGene
20:41 deafferret does this mean something to you? MSG: NT_ contigs are whole chromosome files which are not part of regulardatabase distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.
20:42 Emos deafferet I'm just going to lunch for a small while
20:42 Emos I leave everything connected
20:42 Emos if you want you can send me an email
20:42 Emos e.osimo@gmail.com
20:42 Emos thanks
20:42 Emos be back in half an hour
20:49 deafferret Emos: http://github.com/jhannah/sa​ndbox/blob/master/emos/x.pl
20:50 deafferret Per previous message, looks like NCBI doesn't want you downloading NT_025741.15 all willy-nilly
20:51 deafferret 75224524 bp. woof.
20:53 deafferret wow. 1h 40m of helping people today. increased focus on paying $mortgage  :)
23:07 deafferret Emos: yup. So, back to 2.5 hours ago: looks like NCBI doesn't want you downloading NT_025741.15 all willy-nilly
23:07 deafferret how many of these are you up against?
23:07 Emos isn't it possible to download from 100 to X bp?
23:08 deafferret I don't know if NCBI has any such API
23:08 deafferret do they?
23:08 Emos I would like to automate a script that annotates in a multifasta
23:08 deafferret it's not really a BioPerl question, unless (1) NCBI does have one and (2) someone wrote a hook for that in BioPerl
23:09 deafferret ya. so what you need is someone (NCBI or whoever) to allow downloading of mere ranges of humongous sequences
23:09 deafferret or you need to build up your own local database of those and pull those sequences off your own disk
23:10 deafferret (we maintain 166GB of local databases... eek)
23:10 deafferret is your stuff all from a single organism?
23:10 Emos homo
23:10 Emos yes
23:11 deafferret k. so you could download the latest human assembly from UCSC or wherever, and then pull everything off local disk?
23:11 Emos yes, if it is the only solution I can do that
23:12 Emos is it easy then?
23:12 alper_ joined #bioperl
23:12 deafferret -shrug-  I don't know if it's the only solution. But that error message is telling you that NCBI doesn't let the default API stream 75M bp whenever anyone asks for it
23:13 Emos ah ok
23:13 deafferret so is what you need in here somewhere?  ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/
23:14 deafferret NT_025741.15 and whatever else you're going to want?
23:14 Emos I will use it on many sets of genes
23:15 deafferret and/or maybe ENSEMBL has an API... or... (I don't know)
23:16 Emos http://www.ensembl.org/info/do​cs/api/core/core_tutorial.html
23:19 deafferret hmmm   $slice = $slice_adaptor->fetch_by_region( 'chromosome', '20', 1e6, 2e6 );
23:20 deafferret how much flanking did you want?
23:20 Emos 100k
23:20 Emos my $slice = $slice_adaptor->fetch_by_gene_stable_id( 'ENSG00000099889', 5e3 );
23:20 Emos there's also this one
23:20 Emos now I'm trying to install the ensembl api
23:20 deafferret ya. so does that work? -ponder-
23:21 Emos but cpan doesn't find it
23:21 deafferret Download BioPerl 1.2.3   ??? yee-gods that's insanely old
23:32 deafferret gak. 1.2.3 is Sep 2003. ouch. I don't know what to tell you about that.
23:33 deafferret I don't see any newer adoption, nor any other language (outside of Perl)
23:39 Emos http://doc.bioperl.org/releases/bioperl-​current/bioperl-live/Bio/DB/GenBank.html
23:41 rbuels are you guys talking about the ensembl api using a really old bp?
23:41 deafferret Emos: oh. this slice stuff works fine against a modern BioPerl.
23:42 deafferret so ignore that 1.2.3 nonsense
23:42 * rbuels reaches for the shock collar remote
23:42 * deafferret whimpers
23:43 deafferret rbuels: YES, THAT IS WHAT WE'RE TALKING ABOUT! MERCY!!
23:43 rbuels lol
23:43 Emos oh, but I cannot install it
23:43 Emos how did you install the ensembl api?
23:44 deafferret I didn't I just downloaded it and threw the path in $PERL5LIB
23:44 Emos PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
23:45 Emos ?
23:45 Emos or setenv PERL5LIB ${PERL5LIB}:${HOME}/src/bioperl-live
23:45 Emos ?
23:45 rbuels depends on which command shell you use
23:45 Emos terminal in mac os x
23:45 rbuels those are two different syntaxes for two different command shells
23:45 deafferret export PERL5LIB=${HOME}/src/bioperl-l​ib:${HOME}/src/ensembl/modules
23:45 rbuels terminal is a terminal emulator, and inside of it runs a command shell
23:46 rbuels by default, it's bash i think
23:46 rbuels isn't it?
23:46 deafferret whatever works is the one you should use  :)
23:46 * deafferret barks
23:46 * deafferret yelps
23:46 rbuels lol wtf
23:46 Emos but if I downloaded and unpacked the files in usr/bin/ensembl
23:47 deafferret Oops... I meant bioperl-live up there
23:47 deafferret well, they're not bin, but if that's where you put 'em, then ${HOME}/usr/bin/ensembl/modules
23:48 Emos ok I got it
23:49 deafferret grr  can't fetch NT_025741.15 nor NT_025741 -- it's not a contig or a supercontig??
23:49 * deafferret shakes his fist at Ensembl
23:50 deafferret hmm... website says contig
23:51 Emos I did that
23:52 Emos >export PERL5LIB=${HOME}/src/bioperl-l​ib:${HOME}/src/ensembl/modules etcetera
23:52 Emos etcetera
23:52 Emos but
23:52 Emos Can't locate Bio/EnsEMBL/Slice.pm in @INC
23:52 Emos ...
23:52 deafferret echo $PERL5LIB
23:53 Emos ??
23:53 deafferret type echo $PERL5LIB and paste that
23:53 Emos nothing
23:53 deafferret so setenv
23:54 Emos setenv command not found
23:55 deafferret http://github.com/jhannah/sandb​ox/blob/master/emos/ensembl.pl
23:56 deafferret I don't have a Mac here so I can't help. My Macs are all at home.
23:56 deafferret dunno why NT_025741.15 is being douchey
23:57 Emos Can't locate Bio/EnsEMBL/Registry.pm in @INC (
23:57 Emos ...
23:57 deafferret if you can't get PERL5LIB set then...
23:57 deafferret use lib "/Users/yourusername/src/ensembl/modules";   in your prog
23:58 deafferret or perl -I/Users/yourusername/src/ensembl/modules yourscript.pl
23:59 deafferret I'd email the ensembl-dev mailing list the URL above and see if they can tell you whats up
23:59 Emos is it possible that I don't have perl5lib installed?

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