Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-09-22

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All times shown according to UTC.

Time Nick Message
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08:06 Kaske I have a question regarding BioPerl::Graphics, what settings in a track can i make so that each feature in the track gets its own line (atm. if there is room for two features in same line, they are put together)?
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15:12 perl_splut only way for every track to have its own line is to create a new track for each line
15:13 perl_splut http://www.bioperl.org/wiki/HOWTO:Graphics
15:23 Kaske ok, thanks... a bit strange tho
15:25 perl_splut not really
15:25 perl_splut it keeps the image smaller to keep things on a line if there is room
15:26 Kaske yes, but can be hard to distinguish when having connected features on the same line as a non-connected one
15:26 Kaske making the non-connected look connected
15:26 perl_splut depends on how you draw the connected ones
15:27 Kaske can i put like a padding or something on my connected ones so they have some room to the closest neighbour?
15:27 scottcain Kaske, I missed the beginning of this discussion.  Do you have an example image that you could point to?
15:27 Kaske i can make one quickly, but need to find somewhere to upload it
15:28 scottcain Kaske: example code would be good too.
15:29 scottcain About adding padding: in BioGraphics speak, padding is for edges of the image, not for buffer around individual glyphs, so that's not what you need.
15:30 perl_splut bump
15:31 Kaske http://kaskelothval.users.wh​itehat.dk/connected-ests.gif <-- example on the connected and non-connected
15:31 scottcain perl_splut: ++ I was just looking up the semantics of bump
15:32 perl_splut would probably help if you added a description to each EST, Kaske
15:32 perl_splut then it would be more obvious which are or aren't connected. Though the connected ones have a bunch of ... linking them
15:33 scottcain bump: "by default, they will just overlap.  A bump value of +1 will cause overlapping glyphs to bump downwards" from Bio::Graphics::Panel pod. +2 will put each feature on its own line.
15:34 perl_splut ahh, never noticed the +2 option before...
15:36 Kaske tried +2, but it made the same output as the link i gave... adding descriptions to each est will complicate overview as some will have thousands of ESTs
15:36 Kaske ah... nvm
15:36 Kaske sec
15:38 Kaske nop, didn't do anything
15:38 scottcain Is this your perl script or GBrowse?
15:39 Kaske perl script
15:39 scottcain can you post it with example data?
15:42 Kaske I am afraid i cannot atm. but has bump +2 been implemented in bioperl 1.2.3? (im using an ancient version it seems)
15:43 scottcain Oh, then I can't help you.  I haven't used 1.2.3 in many years :-(
15:44 Kaske I will get it upgraded and try again. Thanks so much for your time!
15:46 scottcain Kaske: when you update, be sure to get the most recent Bio::Graphics too: BioPerl and BioGraphics are separate packages now.
15:47 Kaske right, thanks
15:50 Kaske now that i've found this channel i actually have another questions that has been bugging me... what does this last arrow (to the right) mean on this feature: http://kaskelothval.users.wh​itehat.dk/feature-arrow.gif
16:04 perl_splut check the SeqFeature that is making that track
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16:08 scottcain Kaske: my guess is the strand is wrong on one or more of the features.
16:09 perl_splut not necessarily wrong
16:09 perl_splut I've seen genes that are made of pieces on opposing strands
16:09 Kaske transsplicing events? interesting :)
16:10 Kaske i think this is wrong tho, will look into the strand annotation
16:10 pyrimidine Kaske: if you are using bioperl 1.2.3 you are using a version that is over 7 yrs old
16:10 pyrimidine we don't support it anymore
16:10 pyrimidine (even if ensembl insists on you installing it :)
16:11 Kaske that is probably why I installed it... I however do not have permissions to upgrade it, so i will have to get the administrator to do that :)
16:11 pyrimidine Kaske: look into using local::lib
16:11 perl_splut you can install BioPerl into your own home directory
16:12 perl_splut so you won't affect the system
16:12 CIA-135 bioperl-live: Carnë Draug master * r8f9089f / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences - http://git.io/35CAoQ
16:12 Kaske i tried that to install locally, but CRAN does not agree with my permissions it seems
16:12 pyrimidine CRAN?  Or CPAN?
16:12 Kaske CPAN
16:13 pyrimidine what version of perl are you using?
16:13 perl_splut by default CPAN tries to install to the system folders
16:13 * pyrimidine has fingers crossed it's fairly new
16:13 perl_splut which only root is usually able to do
16:13 Kaske very good question :P is there a command to check it?
16:13 perl_splut perl -V
16:13 perl_splut or perl -v
16:13 pyrimidine perl -v
16:14 Kaske v5.8.8
16:14 pyrimidine must be CentOS
16:14 pyrimidine or RHEL
16:14 pyrimidine they never upgrade
16:14 Kaske probably, i admit i know very little about the servers as im just a master student being granted a bit of access :P
16:15 perl_splut cat /etc/redhat-release
16:15 Kaske CentOS 5.7 yes
16:15 pyrimidine you can still install a local version of your modules, and even an updated version of perl if you want (I generally do that)
16:16 Kaske ok
16:16 pyrimidine but, look seriously into using local::lib, should work with perl 5.8.8
16:16 pyrimidine http://search.cpan.org/perldoc?local::lib
16:17 pyrimidine follow the directions for bootstrapping, which sets pretty much everything up
16:19 pyrimidine IIRC, the latest bioperl from CPAN works with ensembl anyway, not sure why the ensembl folks don't just indicate what breaks (never have specified that)
16:22 Kaske i have a meeting with the systems administrator tomorrow, i'll speak with him before i local install :) but thanks for the pointers, i guess i should stop asking questions until i've upgraded ;)
16:23 pyrimidine Kaske: never hurts to ask
16:30 rbuels pyrimidine: chrisdag is in the room with me, if you want me to say or do anything to him
16:30 rbuels ;-)
16:32 * rbuels is at http://aws.amazon.com/genomicsevent
16:36 Kaske i've made a rough cutout of the code making the above feature (with arrows in both directions): https://gist.github.com/661d14a4e61076542317 as data is taken from a mysql database i can't make a simple example dataset. The output: http://kaskelothval.users.wh​itehat.dk/feature-arrow.gif
16:38 Kaske Howcome i get an arrow to the right? The last feature in the list has a strand of -1
16:39 perl_splut did you check all the features?
16:39 perl_splut and did you check the old documentation on the type of track you are choosing to use?
16:41 Kaske all features in the track are strand "-1". I have not checked the documentation, but it only does it for minus strand features, so i suspect theres something i've missed
16:41 perl_splut or you just don't notice it on 0 or +1 strand objects
16:42 Kaske possibly
16:44 Kaske i need to get some food, so i have to go. Thanks for all your suggestions and help all of you :)
16:47 pyrimidine rbuels: say hi to chrisdag for me (haven't met him in person yet, keep missing him at confs)
16:48 rbuels ok
17:04 pyrimidine rbuels: ask chrisdag if he is responsible for testing.open-bio.org (buildbot for open-bio)
17:04 rbuels pyrimidine: ok i will.  he's talking now though.
17:53 deafferret ooOo.. o
18:20 CIA-135 bioperl-live: Carnë Draug master * rcbc5cd5 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: small fixes on POD documentation - http://git.io/yqCfMA
18:20 CIA-135 bioperl-live: Carnë Draug master * r77c7e35 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: typo on all instances of var name (fixing aesthetic only) - http://git.io/m1NZKQ
18:20 CIA-135 bioperl-live: Chris Fields master * r2740991 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl :
18:20 CIA-135 bioperl-live: Merge pull request #24 from carandraug/bp_genbank_ref_extractor
18:20 CIA-135 bioperl-live: genbank_ref_extractor - http://git.io/e5wJoQ
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