Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-12-15

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All times shown according to UTC.

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00:16 subanark_ Does anyone know if there is a limitation to how big a sequence can be for it to be displayed in gbrowse?
00:17 deafferret subanark_: if you let gbrowse display summaries then you can display genomic sequences in gbrowse easily
00:17 deafferret it zooms in and out
00:17 deafferret are you using a gff file, or...?
00:18 subanark_ I have a .gff and a .fa file
00:18 subanark_ but the info from the .fa isn't being displayed
00:18 deafferret how big is the .gff file?
00:18 subanark_ Only a few lines
00:18 deafferret how big is the .fa file?
00:18 subanark_ I think each sequence is 17kb
00:20 deafferret oh, that's nothing  :)
00:20 subanark_ Yea, its pretty short
00:20 subanark_ But when I click on a strand I don't get the dna sequence
00:21 deafferret ya, let me find you the wiki page I wrote a year ago or so
00:21 subanark_ I'm not sure if the gff is correctly pointing to the fasta, or what the problem is
00:21 deafferret here's the BioPerl solution   http://www.bioperl.org/wiki/Adding_a_DNA_track
00:21 deafferret i'll have to find the gbrowse one
00:22 subanark_ Yea, ideally I want the sequence to be dispalyed directly if you are zoomed in at 100bp
00:23 deafferret ya, that's a gbrowse setting. don't remember the default
00:23 subanark_ I'm sure I know how to get gbrowse to display it, if it could connect the sequence up with the fasta
00:24 subanark_ I have 3 sequences along with primers
00:24 deafferret hmm... it's this   http://search.cpan.org/~lds/Bio-Graphi​cs-1.994/lib/Bio/Graphics/Glyph/dna.pm
00:25 deafferret still need to find the gbrowse tut that talks about it
00:26 deafferret ahh... http://iubio.bio.indiana.edu/gmo​d/gbrowse/tutorial/tutorial.html
00:27 deafferret 11. Displaying DNA and 3-frame translations
00:27 subanark_ I"ve read though that... its just for some reason I can't seem to get the fasta data to connect with the gff3 file
00:28 deafferret did you try the volvox example?
00:28 subanark_ volvox seems to work
00:28 subanark_ I think its just bulking at large sequences
00:29 deafferret hmm... at that point I usually start changing one line at a time from volvox to what I actually want
00:29 deafferret nah, I've thrown whole genomes at it
00:29 deafferret it gets slow (using flat files), but it works
00:30 subanark_ were you able to click on one of the large strands and get the sequence data?
00:31 deafferret I don't recall using that feature
00:31 deafferret "large strands" ? I only ever had one .fa file
00:31 deafferret you can't do contigs / reads, I don't think
00:32 subanark_ one of the entries is large
00:32 deafferret at least I don't think you could a year ago, the last time I touched this stuff
00:32 subanark_ it seems like you have to have a reference sequence and then map others to it, in order to have them displayed together
00:34 subanark_ E.g. http://gmod.eecs.wsu.edu/cgi-bin/g​browse_details/primer2?feature_id=​5;ref=combined;start=1;end=174341 displays no sequence data
00:34 subanark_ http://gmod.eecs.wsu.edu/cgi-bin/gbrowse_details/​volvox?feature_id=37;ref=ctgA;start=1000;end=2000 (from volvox) does
00:48 deafferret hmm... not sure how they did that... is that part covered in the tutorial?
00:48 deafferret that's pretty slick. I wonder if that's just one .fa file or some other feature
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00:54 subanark_ Its not modified, I'm not sure if it is in the tutorial or what... my boss just pointed it out and said, make our data do that
00:54 deafferret when you drop down to "Show 100 bp" -- that's the dna glyph I'm used to
00:55 deafferret the click on features thing I've never done, so don't know how that works
00:55 deafferret subanark_: ya. /me hugs $boss  :)
00:55 deafferret PM mtg starts in 5 minutes so I'll be disappearing without warning shortly
00:55 subanark_ well, thats not as important, but if it can't see the fasta data, it won't dispaly any necu data when graphing
00:56 deafferret umm... your .gff file is where all your drawable items live, as far as I know
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00:56 deafferret so there's one line per thing that gbrowse is supposed to draw in that .gff file
00:57 subanark_ If you look at the EST in volvox you will see the sequence (http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/volvox/)
00:58 subanark_ wait... its the DNA/GC content track
00:58 subanark_ although I guess the ESTs do show that at 100 mp too
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05:02 Shea Hey, do you guys know of any phylogeny/cladogram programs that don't suck?
05:03 Shea I've been trying a bunch lately and they're all pretty terrible.
05:07 deafferret phylip?
05:08 Shea I was using phylip for a while, and it's good for smaller trees, but after a while it reaches a limit
05:08 Shea There seems to be a limit of 3500 by 3500 pixels for its output
05:08 deafferret huh. I haven't done anything heavier-weight than that
05:08 Shea Which puts an effective limit of about a couple hundred nodes.
05:08 deafferret http://www.visualcomplexity.com ?
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05:09 Shea I haven't seen that. I'll try it, thank you.
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05:29 Shea That page has a few cool things on it, but I can't find quite what I'm looking for. :/
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16:07 Biome biome: Chris Fields master SHA1-cc05033
16:07 Biome simple Segment-based type
16:07 Biome http://bit.ly/7CzLZ0
16:07 Biome biome: Chris Fields master SHA1-96250e7
16:07 Biome add simple Segment class
16:07 Biome http://bit.ly/6STEtf
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17:08 * deafferret feeds the phant
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