Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-02-11

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All times shown according to UTC.

Time Nick Message
01:14 deafferret true or false: sound travels faster through a gas than through a liquid
01:15 deafferret Sound travels faster in liquids and non-porous solids (5,120 m/s in iron) than it does in air, traveling about 4.3 times faster in water (1,484 m/s) than in air at 20 degrees Celsius.   http://en.wikipedia.org/wiki/Speed_of_sound
01:15 deafferret apparently I fail 3rd grade Physics
01:25 rbuels congratulations
01:26 thephant and congrats from me too!
01:26 deafferret rbuels: did you know that?
01:26 rbuels yep.
01:26 rbuels so did the phant.
01:27 rbuels he would never forget.
01:27 * deafferret sighs, sepikus
01:27 rbuels seppuku?
01:27 deafferret no, sepikus
01:28 rbuels http://www.youtube.com/watch?v=VV6axfVxpTA
01:29 deafferret tampamu!
01:30 deafferret hmm... how does google index Seppuku - Wikipedia as the first hit for 'sepiku' ?
01:30 deafferret impressive
07:04 bag joined #bioperl
12:37 robkinyon joined #bioperl
12:38 robkinyon anyone interested in the YAPC::NA::2010 CFP?
16:48 faceface cheers
16:49 faceface rbuels: around?
16:51 faceface I've got a pain in the assets
16:52 faceface what can I do with data like this?
16:52 faceface score         queryName              hitName  qs  qe    hs    he phase  bases ident length
16:52 faceface 379 Dart-03P_01_O16.f PGSC0003DMB000000296 118 611 85003 85498     F    494 94.94   1307
16:52 faceface 363 Dart-03P_01_O16.f PGSC0003DMB000000296 118 548 76081 76511     F    431 96.75   1307
16:52 faceface 232 Dart-03P_01_O16.f PGSC0003DMB000000296 326 611 80646 80931     F    286 96.50   1307
16:52 faceface 230 Dart-03P_01_O16.f PGSC0003DMB000000296 316 611 87151 87445     F    296 92.23   1307
16:52 faceface 136 Dart-03P_01_O16.f PGSC0003DMB000000296 116 276 80483 80644     F    161 96.27   1307
16:52 faceface 37 Dart-03P_01_O16.f PGSC0003DMB000000296  76 115 76021 76060     F     40 97.50   1307
16:52 faceface 34 Dart-03P_01_O16.f PGSC0003DMB000000296  76 115 80425 80464     F     40 95.00   1307
16:52 faceface 34 Dart-03P_01_O16.f PGSC0003DMB000000296  76 115 84942 84981     F     40 95.00   1307
16:52 faceface 379 Dart-03P_01_O16.r PGSC0003DMB000000296 573  80 85003 85498     C    494 94.94   1358
16:52 faceface 363 Dart-03P_01_O16.r PGSC0003DMB000000296 573 143 76081 76511     C    431 96.75   1358
16:52 faceface 232 Dart-03P_01_O16.r PGSC0003DMB000000296 365  80 80646 80931     C    286 96.50   1358
16:52 faceface 230 Dart-03P_01_O16.r PGSC0003DMB000000296 375  80 87151 87445     C    296 92.23   1358
16:52 faceface 136 Dart-03P_01_O16.r PGSC0003DMB000000296 575 415 80483 80644     C    161 96.27   1358
16:53 faceface 37 Dart-03P_01_O16.r PGSC0003DMB000000296 615 576 76021 76060     C     40 97.50   1358
16:53 faceface 34 Dart-03P_01_O16.r PGSC0003DMB000000296 615 576 80425 80464     C     40 95.00   1358
16:53 faceface 34 Dart-03P_01_O16.r PGSC0003DMB000000296 615 576 84942 84981     C     40 95.00   1358
16:53 faceface just ignore it and hope it goes away?
17:31 deafferret faceface: what's wrong with it?
17:55 faceface deafferret: nothing wrong with it, its just confusing my analysis
17:55 faceface all these little short tandem duplications that I want to wrap up into one 'HIT'
17:55 faceface all these short little tandem duplications that I want to wrap up into one 'HIT'
17:55 faceface oh wait, above that isn't the problem
17:56 faceface above is just a 'tiling' issue
17:56 faceface but every time I look at the tiling module, something bad happens in my brain
17:56 faceface I don't think it cares if the HSPs are separated by 700kb
17:56 faceface but I do
17:57 deafferret what programs are you using?
17:57 faceface I'd like to 'tile' the above examples where the gap between the HSPs is 'small', and I'd like to remove / resolve spurious HSPs due to tandem duplications
17:57 faceface I was about to say 'perl'
17:57 faceface I'm using SSAHA2
17:58 * faceface points deafferret at SEQwiki :-D
17:58 faceface (for a reference to SSAHA2)
18:03 deafferret google has lots of hits for 'SEQwiki'
18:04 deafferret seqanswers.com ?
18:06 faceface yup
18:08 deafferret so you're doing assembly with a reference in Perl?
18:08 faceface no
18:08 faceface the sequences I have are sequence markers. I need to find their position on the reference
18:09 faceface I'm using ssaha to do the mapping, and perl to untangle all the hits
18:09 deafferret ah. k.    http://www.sanger.ac.uk/resources/software/ssaha2/
18:14 * faceface appologies for the seqwiki round trip
18:14 faceface I just wanted to show you the site
18:16 deafferret no worries.
18:25 pyrimidine joined #bioperl
18:26 * deafferret waves
18:26 pyrimidine o/
18:28 rbuels O HAI
18:28 pyrimidine \o
18:29 * pyrimidine left arm was tired
20:20 driveby_bot joined #bioperl
20:20 driveby_bot /home/svn-repositories/bioperl: r16833 (cjfields) : add a few comments
20:20 driveby_bot Diff: http://tinyurl.com/ydtuoow
20:21 deafferret pyrimidine++
21:21 dnewkirk joined #bioperl
22:26 pyrimidine left #bioperl

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