Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-29

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All times shown according to UTC.

Time Nick Message
00:00 dnewkirk Strawberry Perl 10.04 compiles both Bioperl 1.6.1 and BIoperl-run 1.6.1 just fine, albeit in XP
00:00 newtobioperl wow tahnks dnewkirl
00:00 newtobioperl dnewkirk
00:00 newtobioperl all i have to do is to install Strawberry right?
00:02 dnewkirk yes, install strawberry perl, then enter the command prompt (ideally as admin I'd imagine on windows 7), and then type cpan, install CJFILEDS/BioPerl-1.6.1.tar.gz and then your on your way
00:02 dnewkirk add -run after BioPerl to install the second
00:03 newtobioperl do I have to uninstall Activeperl before I install Strawbeery
00:04 dnewkirk It's the better way to do it to prevent conflicts
00:04 dnewkirk do you have other programs requiring activeperl?
00:05 newtobioperl well, i am using Eclipse as a Perl Editor
00:06 newtobioperl but i think it should be ok to uninstall active perl
00:06 dnewkirk that shouldn't make a difference I don't think
00:06 dnewkirk are you using epic?
00:07 newtobioperl yes
00:08 dnewkirk it calls the interpreter from PATH, so strawberry should be fine, activestate isn't necessary
00:09 newtobioperl thank you so much
00:09 newtobioperl Iam still in the process of installing Bioperl-live
00:09 newtobioperl if this fails, ill try strawberry
00:10 dnewkirk no problem
00:11 dnewkirk Strawberry Perl was designed to interface well with CPAN and build modules on the fly.
00:12 dnewkirk activestate is a great distro for Perl, it just tends to not compile things as well.
00:12 newtobioperl how long does it take to install bioperl-live :)
00:12 newtobioperl it keeps asking me install all bunch of things
00:12 dnewkirk well, it could take 10-15 minutes
00:12 dnewkirk windows is a lot slower than linux in that regard
00:13 dnewkirk there are prerequisites that you may have to install in order to allow all the modules to run
00:14 dnewkirk you don't need to install all potential modules, only stag and a few others
00:14 newtobioperl i already installed stag
00:14 dnewkirk ok
00:14 newtobioperl and i dont know the rest
00:15 newtobioperl i just hit Yes
00:15 dnewkirk hmm
00:15 dnewkirk are you at the testing phase?
00:15 newtobioperl like Convert::Binary::C
00:15 newtobioperl no
00:15 newtobioperl it still asking me to install alot of modules
00:16 newtobioperl now scalar
00:16 dnewkirk ok, you should keep the default answer, so just hit enter instead typing yes, particularly for the first question
00:17 newtobioperl i think its done but i got an error message
00:18 newtobioperl basically some modules failed to install
00:18 dnewkirk ok
00:18 dnewkirk strawberry is probably your better bet at this point :/
00:20 newtobioperl i am running "perl Build test"
00:21 newtobioperl aftere i install CJFILEDS/BioPerl-1.6.1.tar.gz on strawberry, does  it automaticallly add bioperl-run for me?
00:21 dnewkirk no, you'll install them each individually
00:22 newtobioperl using cpan?
00:22 dnewkirk once the first completes, type "CJFIELDS/BioPerl-run-1.6.1.tar.gz"
00:22 dnewkirk yes
00:22 dnewkirk you can just call cpan fromt eh command prompt
00:22 newtobioperl CJFILEDS is my folder dir?
00:23 dnewkirk mm,  no, it's the directory in the cpan repository
00:23 dnewkirk so, open a command prompt, then type in cpan
00:23 dnewkirk That gives you a direct interface with cpan
00:23 newtobioperl Result: FAIL. Failed 7/344 test program,. 10/18023 subtests failed
00:24 newtobioperl i guess i have to switch to strawberry
00:24 dnewkirk but you had a failed module I'm assuming
00:25 newtobioperl well, i am taking a break
00:25 dnewkirk ok
00:25 newtobioperl and then start installing strawbeery
00:25 newtobioperl thank you so much for helping dnewkirk
00:25 dnewkirk you welcom
00:25 newtobioperl ill be back
00:25 dnewkirk e
00:49 dnewkirk deafferret?
00:50 dnewkirk be back on in an hour newtobioperl, making my way home
01:06 brandi joined #bioperl
01:07 brandi left #bioperl
01:11 deafferret hmm?
02:15 dnewkirk joined #bioperl
02:25 dnewkirk any luck newtobioperl?
02:27 newtobioperl i am still downloading strawberry
02:27 newtobioperl almost done
02:27 newtobioperl just uninstall activeperl
02:28 newtobioperl i have a question
02:28 newtobioperl i have to write a program where i have to search through human genome with thousands of queries
02:29 newtobioperl do you know any algorithm that allows me to that in a shortest time?
02:29 newtobioperl in my lab, we have a new HIV database
02:29 newtobioperl this database includes thousands of clusters
02:30 newtobioperl i have to design an application to know where these clusters are in human genome
02:30 newtobioperl to find*
02:32 dnewkirk What sort of alignment are you needing to do?
02:33 newtobioperl i need to know where those clusters are in Human genome (start pos-end position)
02:34 dnewkirk hmmr 3 has been used to do that type of work, and there was a wrapper/parser for it in Bioperl...
02:34 newtobioperl its like BLAT output but can perform with thousands of queries
02:34 newtobioperl you mean BLAT wrapper?
02:35 dnewkirk http://hmmer.janelia.org/
02:35 deafferret dnewkirk: were you looking for me?
02:36 dnewkirk nothing important, was just going to see if you were available to help while I was on my way home is all
02:37 deafferret ah. he didn't speak while you were gone, so I snuck off the hook apparently   :)
02:37 newtobioperl :sigh: fail to install CJFILEDS/BioPerl-1.6.1.tar.gz
02:37 deafferret I know zero about Windows, so I doubt I can be any help
02:38 deafferret the only thing I know about it is my burning hatred
02:38 newtobioperl i hate windows now
02:38 dnewkirk Is there a particular error perchance?
02:38 newtobioperl i have been trying to install bioperl-run
02:38 newtobioperl for the whole day
02:40 dnewkirk Did you right-click and open the command prompt as administrator?
02:40 deafferret or install linux?  :)   <-- still failing to be helpful
02:40 newtobioperl well, when I run the cmd
02:41 newtobioperl on the window title, it says "Adminitration ..."
02:41 newtobioperl "adminitrator..."
02:41 dnewkirk ok, so that should be fine.
02:41 newtobioperl and strawberry is mean
02:42 newtobioperl "no success downloading "C:\strawberry\cpan\.,.....". Giving up on it
02:42 dnewkirk ?
02:43 newtobioperl thats one of the errors I got when i tried to install  CJFILEDS/BioPerl-1.6.1.tar.gz
02:44 dnewkirk when typed in cpan, what version is it?
02:44 dnewkirk in the command prompt that is
02:44 newtobioperl here is the error http://img149.imageshack.u​s/img149/4074/61983783.png
02:44 newtobioperl v1.9456
02:45 dnewkirk so its the latest
02:45 dnewkirk mm, the screenie is a little small :p
02:45 newtobioperl i have been installing and uninstalling bunch of things on my computer
02:46 newtobioperl lets me restart it
02:46 newtobioperl maybe it helps
02:46 newtobioperl oh sorry
02:46 newtobioperl i didnt know imageshack resize it
02:47 newtobioperl http://img541.imageshack.u​s/img541/1609/37601766.png
02:47 newtobioperl this is better
02:49 dnewkirk hmmm
02:49 dnewkirk that's a bizarre error
02:49 newtobioperl let me restart my computer
02:49 newtobioperl brb
02:49 dnewkirk k
02:55 newtobioperl joined #bioperl
02:57 newtobioperl still got the same error
02:59 dnewkirk my notebook has Windows 7 on it, lemme give it a shot
02:59 dnewkirk what's the exact command you give when trying to install bioperl?
02:59 newtobioperl hold on, i think i can install it this time
03:00 newtobioperl i think I typed the wrong path to Bioperl
03:00 newtobioperl before
03:00 dnewkirk ok
03:01 dnewkirk the C:/ was what was making me think it was looking for it locally..
03:01 newtobioperl it says DONE
03:01 dnewkirk nice!
03:01 newtobioperl scanning cache
03:02 newtobioperl i am still waiting for the cpan cmd line
03:02 dnewkirk it'll take a few minutes
03:03 dnewkirk just let it go, should install without a problem
03:06 newtobioperl dnewkirk, the website that you gave me HMMER
03:06 newtobioperl you used it before?
03:06 dnewkirk I've played with it some
03:07 newtobioperl how is it compare to BLAST and BLAT
03:07 newtobioperl ?>
03:07 dnewkirk for small project. others here have used it much more extensively
03:08 newtobioperl can it handle about 16 thousands of queries?
03:08 newtobioperl on human genome?
03:08 dnewkirk In terms of quality of matches? As good or better than both. In terms of speed? Pretty quick, can be used for more high-throughput queries.
03:09 newtobioperl i always think that BLAT is the fastest one
03:09 dnewkirk It can handle that, yes
03:10 newtobioperl because BLAT index its database
03:10 dnewkirk BLAT is pretty fast, but it lacks some precision as well
03:10 dnewkirk right
03:10 newtobioperl does HMMER index its database too?
03:11 dnewkirk If your looking for quick and dirty placement, BLAT should be fine
03:11 newtobioperl lol
03:13 dnewkirk HMMER does some form of indexing, but I'm not entirely sure of all of the internals
03:24 newtobioperl sorry It failed to instal bIoperl-run again
03:24 newtobioperl http://img248.imageshack.u​s/img248/1074/12477204.png
03:24 newtobioperl i think it needs Bioperl core
03:24 newtobioperl and I dont have it
03:26 dnewkirk so Bioperl-1.6.1 installed, but not Bioperl-1.6.1-run?
03:26 newtobioperl error is here
03:26 newtobioperl http://img248.imageshack.u​s/img248/1074/12477204.png
03:26 newtobioperl btw, how do you know if Bioperl is installed properly?
03:29 dnewkirk A success via cpan should be enough, though you may come across bugs from time to time.
03:29 dnewkirk for individual modules that is
03:31 dnewkirk Did you install Bioperl-1.6.1 first perchance?
03:31 newtobioperl yes
03:32 dnewkirk hmm
03:33 newtobioperl i dont think Bioperl is installed yet
03:33 newtobioperl trying to use Genbank
03:33 newtobioperl but Epic says "Can't locate Bio/DB/GenBank.pm in @INC (@INC contains: D:/eclipswp/.metadata/.plugins/org.epic.debug D:/eclipswp/bioperl C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib .) at D:/eclipswp/bioperl/test.pl line 4."
03:44 dnewkirk I'm trying to install on my laptop, so I'll see what I can figure out
03:45 newtobioperl thank you so much
03:45 newtobioperl i really appreciate your help
03:47 dnewkirk Sorry, it's been awhile since I've used Windows for Perl scripting and everything else, so I'm a little more rusty than I realized, else I might have had the answer ready on the fly...
03:52 newtobioperl I have to be the one who says sorry
03:53 newtobioperl for using WINDOWs
03:54 dnewkirk contrary to popular sentiment, windows isn't that bad. You can do a lot, but you'll always be limited by the need for certain libraries or the ease of compilation for certain programs, that's all.
03:55 newtobioperl When I look at the old activeperl folders, there is a BIO folder in Perl/site/lib
03:55 dnewkirk Microsoft is actually working on developing a bioinformatics consortium
03:55 newtobioperl but that BIo folder is not in Strawberry/Perl/site/lib
03:56 newtobioperl hopefully, they finsih that project soon
04:01 dnewkirk seems to be building fine on my laptop...
04:01 newtobioperl omg
04:01 newtobioperl what am i missing
04:02 newtobioperl do you see BIO folder in strawberry/perl/site/bin?
04:03 dnewkirk in site/lib? yep
04:03 newtobioperl i dont see it in site/lib
04:04 dnewkirk Komodo Edit also finds the modules
04:06 dnewkirk try installing BioPerl again; any time it asks a question regarding prerequisites, just accept the default (which should be fine for what you intend to do I believe).
04:06 newtobioperl sigh
04:06 dnewkirk sorry :/
04:06 dnewkirk it's a little odd
04:07 newtobioperl maybe i have been installing alot of things on my computer
04:08 dnewkirk i used a registry cleaner after uninstalling activestate on my laptop, and it didn't have to make any fixes. The activestate uninstaller does an excellent job at cleaning up.
04:10 newtobioperl i am reinstalling active perl
04:10 newtobioperl see how it goes
04:15 dnewkirk the strawberry perl website has a link to an irc channel at the top, and you might be able to get some help from there as well
04:15 newtobioperl oh yeah
04:15 newtobioperl i see it
04:16 dnewkirk you can log on directly from the browser
04:18 newtobioperl i just run "nmake test"
04:18 newtobioperl and it says successfuly
04:19 newtobioperl Result: PASS
04:19 newtobioperl but i still dont see the bIo folder in the lib
04:19 newtobioperl werid
04:19 dnewkirk oooohhhhh
04:19 dnewkirk did you do nmake install?
04:19 newtobioperl no i didnt
04:20 newtobioperl i just copie nmake
04:20 dnewkirk your building it directly from the downloaded version?
04:20 newtobioperl to the bin folder
04:20 newtobioperl i use CPAN
04:20 newtobioperl to install
04:20 newtobioperl cpan> install ..../Bioperl...
04:22 dnewkirk Sorry if I'm asking the "Did you plug in the unit" kinds of questions :p
04:23 dnewkirk hmm
04:23 pyrimidine joined #bioperl
04:23 pyrimidine dnewkirk: you guys still here?
04:23 dnewkirk yep, still trying to get him up and running
04:23 dnewkirk :/
04:24 dnewkirk his machine doesn't like bioperl
04:24 pyrimidine Does help to spell my name correctly
04:24 dnewkirk apparently
04:24 dnewkirk :)
04:26 dnewkirk Strawberry works well for my machines, but it installs bioperl on his, but it's not ending up in @INC, which is odd.
04:26 newtobioperl my comp really hates Bioperl
04:26 pyrimidine that is odd
04:26 newtobioperl i am using Cpan to install Bioperl-run directly
04:27 newtobioperl and my cmd says "Bioperl Minimal core version 1.00600 is required for Bioperl-Run
04:27 newtobioperl i just installed BIoperl 1.6.1
04:28 newtobioperl somehow it keeps Biocore
04:28 pyrimidine what happens when you use 'perldoc -l Bio::Root::Root'?
04:28 newtobioperl lets me try
04:29 newtobioperl perdoc -1 or -L?
04:29 pyrimidine lowercase 'L'
04:29 pyrimidine (for 'location')
04:29 newtobioperl no documentation for
04:30 newtobioperl "-l"
04:30 newtobioperl where should I type it?
04:30 dnewkirk one line
04:31 dnewkirk perldoc -l Bio::Root::Root
04:31 dnewkirk the -l is a flag
04:32 deafferret dnewkirk++ # stamina
04:35 pyrimidine I'm wondering if there is some mixing of two different perl binaries going on here...
04:35 deafferret mmm... sleep
04:35 deafferret &
04:35 pyrimidine sleep is for the weak
04:35 newtobioperl no documentation found for "Bio::Root::Root"
04:35 * pyrimidine is weak
04:35 newtobioperl lol
04:36 dnewkirk activestate got uninstalled, then strawberry installed, so there shouldn't be any binary issues
04:36 * pyrimidine is not sure what the win equivalent to 'which' is...
04:36 pyrimidine Maybe 'where perl'?
04:37 dnewkirk she's a witch! Burn her!
04:37 dnewkirk he uses epic, and it showed the strawberry perl binaries in @inc, and nothering else
04:38 newtobioperl i just reinstall activestate
04:38 newtobioperl when I use "where perl" i got 2
04:38 newtobioperl C:\perl\bin\perl.exe
04:38 newtobioperl and C:\strawberry\perl\bin\perl.exe
04:38 pyrimidine the first one in the path will be used
04:39 pyrimidine you need to remove AS Perl
04:39 newtobioperl i did before
04:39 newtobioperl lets me try again
04:40 newtobioperl then what?
04:40 newtobioperl I and Dnewkirk tried alot of diff way
04:40 newtobioperl s
04:41 pyrimidine what does 'where perl' say now?
04:41 newtobioperl 1 line
04:41 newtobioperl strawberry
04:41 pyrimidine 'perl -V'?
04:41 pyrimidine (that should give you @INC)
04:42 newtobioperl it gives me a list
04:43 newtobioperl platform, complier
04:43 pyrimidine okay
04:43 newtobioperl linker and libraries
04:43 pyrimidine last one is @INC
04:43 newtobioperl @INC:
04:44 newtobioperl C:/strawberry/perl/site/lib
04:44 pyrimidine I guess the key one is 'perldoc -l Bio::Root::Root'
04:44 newtobioperl C:/strawberry/perl/vendor/lib
04:44 newtobioperl lets me see
04:45 newtobioperl no documentation found for "Bio::Root:Root"
04:45 XaeroOne joined #bioperl
04:46 pyrimidine any idea where your bioperl modules were installed?
04:48 newtobioperl i can't find the BIO folder in strawberry
04:49 pyrimidine Makes me think it didn't install
04:49 newtobioperl should I "install CJFIELDS/Bioperl again
04:49 newtobioperl yep
04:49 dnewkirk yep
04:49 pyrimidine yep
04:50 pyrimidine nice thing with CPAN is, if the tests don't pass you can force install it anyway.  The modules are pure perl, and as long as you install the required modules it shouldn't be a problem
04:51 newtobioperl here is the message i got
04:51 newtobioperl http://img339.imageshack.u​s/img339/7408/59937524.png
04:52 pyrimidine odd.  go ahead with it, though.
04:52 newtobioperl running
04:53 pyrimidine this will take a bit of time.  I need to crash for the night, but I will backlog to see if everything worked.
04:53 pyrimidine night! &
04:53 dnewkirk night!
04:53 dnewkirk the checksum issue might be with cpan, I had a similar error earlier myself
04:54 newtobioperl oh
04:54 newtobioperl http://img8.imageshack.us/img8/4375/17457927.png
04:54 newtobioperl after I hit Proceed
04:54 dnewkirk thats ok
04:55 * dnewkirk sends a round of guinness to all
04:55 newtobioperl http://img375.imageshack.u​s/img375/3303/36883780.png
04:55 newtobioperl done
04:56 newtobioperl still no BIO Folder in Lib
04:56 dnewkirk it didn't install
04:56 dnewkirk you'll know when it installs
04:58 newtobioperl ...
04:58 newtobioperl god knows what happens to this thing
04:58 newtobioperl :)
04:58 dnewkirk do you always have eclipse open when you install?
04:59 newtobioperl i dont remember but I have it open this time
04:59 dnewkirk i see the icon on your task bar
04:59 newtobioperl i just close it
04:59 newtobioperl reinstalling bioperl
04:59 dnewkirk k
05:00 newtobioperl something different this time
05:00 newtobioperl lol
05:00 newtobioperl checksums is running
05:01 newtobioperl dnewkirk, are you working now?
05:01 newtobioperl as a Bioinformatic scientist?
05:01 dnewkirk I'm a first year graduate student
05:02 dnewkirk well, second now I guess after passing prelims
05:02 newtobioperl i am still Undergrat
05:02 newtobioperl d*
05:02 newtobioperl this is my research
05:03 newtobioperl its now running
05:03 dnewkirk nice
05:03 newtobioperl http://img251.imageshack.u​s/img251/7990/26069465.png
05:04 newtobioperl here is what happening
05:04 newtobioperl it ran like this before
05:09 dnewkirk that's what we want to see
05:09 newtobioperl FINALLY,
05:09 newtobioperl I see the BIO folder
05:10 dnewkirk quick, install BioPerl-run!
05:10 dnewkirk :p
05:10 dnewkirk before it decides to erase itself from your drive and mock us both :)
05:11 newtobioperl running
05:11 newtobioperl phew
05:12 newtobioperl how can I make sure that Bioperl-run was installed?
05:13 newtobioperl finally,
05:13 newtobioperl phew
05:13 newtobioperl its there
05:13 dnewkirk awesome
05:13 newtobioperl this is how windows run
05:14 newtobioperl why didnt it work before
05:14 newtobioperl should I install bioperl-db and network too?
05:14 dnewkirk not enough eye of newt
05:14 newtobioperl while its working
05:14 dnewkirk I'd wait until you know you need them
05:15 newtobioperl ok
05:15 dnewkirk can't hurt, but you may decide you want some added modules and you'd have to reinstall
05:15 newtobioperl you'r right
05:15 newtobioperl have you ever use BLAT?
05:15 newtobioperl in BIoperl?
05:16 dnewkirk nope, not using the bioperl wrapper
05:20 newtobioperl Dnewkirk, i realy appreciate your help. Without you, i might kill my computer at this point
05:20 newtobioperl i am off to bed. Ill come here more often
05:20 newtobioperl thanks again
05:21 dnewkirk your welcome
05:21 dnewkirk night
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14:07 davidbr Hi, I have calculated a score for each position in a genbank, and I would like to plot this score graph against the genbank. How can I do that
14:08 davidbr (Bioperl newbie)
14:21 kai I'm not sure I understand what you're trying to do
14:23 davidbr just a simple line plot. I have a genomic region of 1000bp and a value for each position (1000 values). I want to plot all those values as a line.
14:25 deafferret http://search.cpan.org/perldoc?GD::Graph  ?
14:26 davidbr but I want them to be aligned to a track showing the genes and other features from the genbank
14:26 davidbr I think xyplot is the answer, but I do not know how to use it.
14:27 davidbr Can I create a sinlge feature with all these values? a feature for each position?
14:27 deafferret a 'track' in what? gbrowse?
14:27 davidbr no, in the plot
14:27 deafferret you want a single graphic with a jillion features plus a line graph?
14:28 davidbr look at the bootom of this: http://cpansearch.perl.org/src/LDS/GBrows​e-2.09/htdocs/tutorial/figures/graph1.gif
14:28 davidbr this is what I want
14:28 deafferret that looks like it was pulled from gbrowse
14:28 deafferret maybe Bio::Graphics directly?
14:28 davidbr so what, can't it be done in bioperl?
14:28 deafferret do you want to zoom in/out and scroll?
14:29 deafferret :)
14:29 davidbr no
14:29 davidbr static
14:29 deafferret bioperl is one piece of the puzzle
14:29 davidbr that's enough for me now.
14:29 deafferret hm?  Bio::Graphics is a separate package from BioPerl
14:30 deafferret http://search.cpan.org/~lds/Bio-G​raphics-2.10/lib/Bio/Graphics.pm
14:31 davidbr ok, that's not really the issue. can you help me?
14:31 deafferret read the doc I just sent you, then ask questions
14:32 davidbr I read it already and did all the simple examples they give.
14:32 deafferret that wasn't a question.  :)
14:32 davidbr the question was already asked multiple times.
14:32 davidbr how do I plot a line graph.
14:33 davidbr add a question mark to that
14:34 deafferret did you add_track( -glyph=>'line')  ?   http://search.cpan.org/~lds/Bio-Graphi​cs-2.10/lib/Bio/Graphics/Glyph/line.pm
14:35 davidbr what feature do I pass to that line?
14:36 davidbr that is, how do I create the feature I need? Is it a single feature? a feature for each bp?
14:37 deafferret "This glyph draws a line parallel to the sequence segment. It is different from other glyphs in that it is designed to work with DAS tracks."   I don't know what a DAS track is. Do you?
14:39 davidbr Nope. http://search.cpan.org/perldoc?Bio%3A%3ADas
14:39 deafferret yup. at a glance I don't know what's going on there
14:39 * deafferret would start with a Google search of "DAS"
14:39 deafferret whatever it is, you can probably gen your own and slurp it somehow
14:39 deafferret this is probably really convenient under certain circumstances. sounds like you're not in that niche
14:40 deafferret so you could poke around inside BioPerl (Bio::* is BioPerl) looking for examples, or simple file readers or .t files
14:40 deafferret oh, Distributed Annotation Service IIRC
14:41 deafferret haven't done any DAS
14:41 deafferret HEAD is here, contributions most welcome.  http://github.com/bioperl/bioperl-live
14:42 deafferret also the bioperl-l mailing list probably hosts people with clues
14:46 davidbr ok, thanks
14:47 * deafferret nods
14:54 newtobioperl i have question. Lets say you have a index file of your database. How can you search in that index file???? What module allows you do that?
14:54 deafferret what database are you using?
14:56 newtobioperl Fasta, i have a fungi fasta
14:56 newtobioperl database
14:56 newtobioperl then I index it
14:56 newtobioperl it produces an index file of that database
14:57 newtobioperl I also have another fasta file (call it query.fasta)
14:57 newtobioperl i want to search all the sequences in query.fasta against that Index
14:57 newtobioperl how can I do that?
14:58 deafferret define 'search'.  blast? exact match?
15:00 newtobioperl blat
15:00 newtobioperl basically, I want to run BLAT
15:00 newtobioperl on the a database (fasta file)
15:00 newtobioperl here is my code
15:01 deafferret i don't know anything about blat (I've forgotten)
15:01 newtobioperl #!/stawberry/perl/bin/perl -w  use warnings; use Bio::Tools::Run::Alignment::Blat; use Bio::SeqIO; use Bio::DB::Fasta;    my $seqio_object  = Bio::SeqIO -> new (-file => 'C:/Users/MINH/Desktop/yeastquery.fasta',  -format => 'fasta');           my $database = 'C:/Users/MINH/Desktop/yeast.nt'; my $db = Bio::DB::Fasta->new($database);           my $factory = Bio::Tools::Run::Alignment::Blat->new();   while (my $blat_object = $seq
15:01 newtobioperl sorry you have to read all of them on the same line
15:01 deafferret please don't paste. use gist.github.com or similar, per http://bioperl.org/wiki/IRC#Getting_help
15:04 newtobioperl https://gist.github.com/457329/1fb84​50fc4f522c6492284f131089f9faf215351
15:05 newtobioperl got this error
15:05 newtobioperl MSG: Blat call ( -out=psl  C:\Users\MINH\AppData\Local\Temp\GZxQEF_YWw C:\Users\MINH\AppData\Local\Temp\oCP0q7Qzmu) crashed: 256
15:05 newtobioperl STACK: Error::throw
15:05 newtobioperl STACK: Bio::Root::Root::throw C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368
15:06 newtobioperl STACK: Bio::Tools::Run::Alignment::Blat::_run C:/strawberry/perl/site/lib/Bio/​Tools/Run/Alignment/Blat.pm:262
15:06 newtobioperl STACK: Bio::Tools::Run::Alignment::Blat::run C:/strawberry/perl/site/lib/Bio/​Tools/Run/Alignment/Blat.pm:178
15:06 newtobioperl STACK: D:/eclipswp/bioperl/readfasta.pl:15
15:06 newtobioperl I am using Window 7, EPIC
15:06 deafferret again: DO NOT paste in channel. thanks
15:07 deafferret can you add that info to the bottom of your gist please? whoever helps will need that
15:07 deafferret I know *nothing* about windows
15:07 deafferret (sorry)
15:08 deafferret have you tried running blat manually outside of bioperl?
15:08 deafferret (Bio::Tools::Run::Alignment::Blat just runs it for you)
15:08 deafferret if blat itself if crashing there is nothing bioperl can do
15:08 deafferret if blat itself is...
15:11 newtobioperl what do you mean running blat manually outside of bioperl?
15:13 deafferret Blat is a program you installed, right?
15:14 newtobioperl oh I have to install Blat seperately?
15:14 deafferret I'm just guessing, I don't know. I assume yes.
15:18 newtobioperl what if I want to write my own program,
15:18 newtobioperl what should I do after I index my database?
15:19 deafferret search it?  :)
15:19 newtobioperl sorry for my english
15:19 newtobioperl my job is
15:19 newtobioperl lets say i have a thousand sequences that I got from HIV data
15:21 newtobioperl I want to know where they are in Human Genome database
15:21 newtobioperl how can I do that?
15:21 newtobioperl example: >HIV 1  AAAGGGCCTTT
15:22 newtobioperl I want to know where AAAGGGCCTTT is in HUman genome
15:22 newtobioperl start position, end position
15:22 deafferret are your sequences really that short? exact match?
15:22 newtobioperl yes
15:22 newtobioperl not really that short
15:22 newtobioperl but they are not long
15:22 deafferret .oO( holy crap! a customer! -laugh- )
15:22 newtobioperl this is for my research
15:22 deafferret you sir, want this thing I wrote called Bio::BroodComb
15:22 newtobioperl lol
15:23 deafferret it does EXACTLY that
15:23 newtobioperl is it in Bioperl?
15:23 deafferret http://github.com/jhannah/bio-broodcomb
15:23 deafferret yup
15:23 newtobioperl is that your picture?
15:23 deafferret yup
15:23 newtobioperl non la'
15:23 deafferret eek... windows
15:23 newtobioperl iam vietnamese
15:23 newtobioperl :)
15:24 deafferret do you have a linux box you can use?
15:24 deafferret BroodComb throws all it's results into an SQLite database
15:24 deafferret here's an example .t file   http://github.com/jhannah/bio-bro​odcomb/blob/master/t/10-subseq.t
15:25 deafferret here's the SubSeq SYNOPSIS  http://github.com/jhannah/bio-broodcomb/​blob/master/lib/Bio/BroodComb/SubSeq.pm
15:25 newtobioperl can it throw its results into a file?
15:25 deafferret well, genome searched take a couple minutes. then you can export your 4M hits to a text file if you want
15:26 deafferret I've been using ensembl datasources recently
15:26 deafferret (a couple minutes meaning... an hour?)
15:27 newtobioperl lol
15:27 deafferret I owe a researcher some human, mouse, and rat already... I could throw in your batch too I guess
15:27 newtobioperl so basically, you need a large-seq and small-seq
15:27 deafferret assuming latest ensembl human reference is ok
15:27 newtobioperl and you hash both of them
15:28 deafferret yup
15:28 deafferret ya. it just does a perl regex match is all
15:28 deafferret you'll have millions, which are thrown into SQLite for you
15:28 deafferret then you can .dump the SQLite results
15:28 deafferret or query them (write reports against that database) or whatever
15:29 deafferret part of my current project is tying the results into ensembl  or gbrowse viewer
15:29 deafferret so you can zoom in/out, pan around the resultset
15:29 newtobioperl wow
15:29 newtobioperl i guess we are working on the same thing except i am a newbie
15:29 deafferret -shrug-  wish I had more time
15:30 deafferret http://biodoc.ist.unomaha.edu/​rt/Ticket/Display.html?id=1045  guest guest
15:30 deafferret http://biodoc.ist.unomaha.edu/wiki/Main_Page
15:31 newtobioperl deafferret, you are a prof?
15:31 deafferret so your reference is "large seq" and your short things are "small seq" and in 10 lines of code you end up with 4M results
15:32 deafferret nope. http://bioperl.org/wiki/User:Jhannah
15:32 newtobioperl in my case, my large-seq is human genome
15:32 deafferret yup
15:32 newtobioperl smallseq is about 16k of HIV clusters
15:32 deafferret that's the same "large seq" I have right now
15:32 deafferret yup. that's *exactly* what Bio::BroodComb::SubSeq was designed to do
15:32 deafferret (exact match)
15:33 deafferret well, I have 3 sets of "large seq" -- human, mouse, rat
15:33 deafferret doing a bunch of miRNA stuff
15:33 deafferret (thousands of miRNAs are my "small seq" right now)
15:33 deafferret millions of hits  -laugh-
15:34 deafferret so the next question is: for those hits, where are they in relation to all other known features?  In exons? in introns? in UTR regions? which? 5'? 3'?
15:34 deafferret etc etc etc   :)
15:34 newtobioperl how long does it take you do thousands of miRNAs?
15:34 deafferret an hour?
15:34 deafferret on a small linux server
15:34 deafferret single CPU
15:35 deafferret we have computer clusters, but don't need them for this
15:37 newtobioperl why do you use regex instead of create an index of the database like BLAT does ??
15:41 newtobioperl brb after 30mins
15:43 deafferret cause I don't care enough to make it hard?  ;)
15:43 deafferret it runs once for an hour, then people argue about the results for 10 years, so runtime doesn't matter to me  :)
15:44 deafferret isn't BLAT designed for longer "small seq" strings anyway?
15:44 deafferret BLAT is BLAST only faster because it's less granular?
15:45 deafferret I'll stop talking now, since I don't know what I'm talking about
16:45 newtobioperl please keep talking deafferrent
16:45 newtobioperl :)
16:46 newtobioperl BLAT index their database
16:46 newtobioperl its faster cuz it uses RAM to perform its task
16:46 newtobioperl BLAST takes its queries and compare to the database
16:47 deafferret well, as I said above I don't care about runtime  :)
16:47 newtobioperl while BLAT takes its database and compare to the queries
16:52 newtobioperl deafferret, how can I set up the SQL for broodcomb?
16:53 deafferret "set up the SQL?"  it creates the database automatically
16:55 deafferret (on linux. I have no idea about windows. you'll need SQLite installed)
16:55 deafferret probably won't work on windows because the filepaths are naive and such
16:55 newtobioperl I have mySQL on my comp
16:55 deafferret if you want to get it working that'd be great
16:55 deafferret BroodComb is SQLite only right now
16:56 deafferret (patches welcome)
16:56 deafferret The whole point of broodcomb is "don't make me do any work, just do everything for me"
16:56 deafferret so on linux, SQLite is an easy default zero-config database
16:56 newtobioperl can you direct me to the part where  Broodcomb's results are
16:56 deafferret sub report1()  ?
16:57 newtobioperl where you export ur results to SQL
16:57 deafferret "export to SQL" ?
16:57 deafferret the results are inserted into SQLite tables. there are basic reports(), or you write your own
16:57 deafferret or just .dump the SQLite database
17:06 newtobioperl The Link on cpan doesnt work
17:06 newtobioperl is it already installed in Bioperl?
17:08 deafferret BroodComb?
17:11 newtobioperl yes
17:14 deafferret BroodComb is not a part of BioPerl, nor has it been uploaded to CPAN. I've never had a customer before.  :)
17:14 deafferret so you use git to 'clone' it. Or I can make you a tarball if you prefer.
17:15 deafferret oh. you can also click 'Download Source' on github and it tarballs it for you  :)
17:15 deafferret deafferret++ # so lazy
17:15 deafferret ha! firefox css problem on that button
17:18 deafferret github++ # laziness enabler
17:22 newtobioperl i gitted it
17:22 newtobioperl but it doesnt have build.pl lol
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17:34 deafferret newtobioperl: nope. there's nothing to build. it Just Works  :)
17:34 deafferret (on linux)
17:34 newtobioperl lol
17:34 deafferret do you have SQLite installed?
17:35 deafferret biab (quick lunch)
17:37 newtobioperl k, talk to you later
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18:38 deafferret back
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18:57 deafferret mmm... Amazon EC2 + Ubuntu
19:01 newtobioperl I want MAC
19:01 newtobioperl deafferret, do you know how Bioperl creates Index file?
19:02 newtobioperl I am looking at Bio::Index::Fasta but it doesnt give me any info about make_index
19:09 deafferret looks like it's just    join "\034", @args    and stored a byte offset
19:09 deafferret Bio::Index::Abstract does the heavy lifting apparently
19:09 deafferret add_record()
19:11 deafferret make_index()
19:14 newtobioperl so then how can I look for a query in an index file?
19:14 deafferret wut?
19:15 deafferret Bio::Index::Fasta is (1) ID (2) Sequence.  I don't think it even does description (does it?)
19:15 deafferret I don't know what you mean by 'query'
19:15 deafferret Bio::Index::GenBank indexes several IDs, which is neato.)
19:19 newtobioperl query means search query, like a sequence in fasta file "AAGGCCTTTGG". What if I want to find where this sequence is in the index file
19:19 newtobioperl can I do that?
19:19 deafferret nope. it indexes on ID, not sequence.
19:19 deafferret if you want to index on sequence, throw them both in SQLite
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19:51 CIA-95 bioperl-live: Chris Fields topic/species_proxy * rb1f8cfe / (Bio/Species.pm t/Species.t): revert species to the prior version (all tests now pass) - http://bit.ly/aDjmyt
19:54 CIA-95 bioperl-live: Chris Fields master * rf1cea60 / Bio/SeqIO/genbank.pm : add ss-RNA to allowed moltypes - http://bit.ly/dqxZfY
19:58 CIA-95 bioperl-live: Chris Fields master * rfbc8f9a / t/RemoteDB/SwissProt.t : remote database change (ensembl ID not present in mapper any more) - http://bit.ly/cEkvzP
20:06 yomimono joined #bioperl
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21:03 CIA-95 bioperl-live: Chris Fields topic/species_proxy * rf1cea60 / Bio/SeqIO/genbank.pm : add ss-RNA to allowed moltypes - http://bit.ly/dqxZfY
21:03 CIA-95 bioperl-live: Chris Fields topic/species_proxy * rfbc8f9a / t/RemoteDB/SwissProt.t : remote database change (ensembl ID not present in mapper any more) - http://bit.ly/cEkvzP
21:03 CIA-95 bioperl-live: Chris Fields topic/species_proxy * rd14fe40 / (Bio/SeqIO/genbank.pm t/RemoteDB/SwissProt.t): Merge branch 'master' into topic/species_proxy - http://bit.ly/9K1tMr
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21:25 CIA-95 bioperl-live: Lincoln Stein master * re96a873 / (4 files): added routines to fetch all seqids - http://bit.ly/bEOXiR
21:25 CIA-95 bioperl-live: Lincoln Stein master * rc0b0e50 / (13 files in 10 dirs): Merge branch 'master' of git@github.com:bioperl/bioperl-live - http://bit.ly/9ARWAe
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