Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-29

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:20 dnewkirk joined #bioperl
00:20 dnewkirk \clear
00:20 dnewkirk :p
00:45 dnewkirk Does anyone regularly use sqlite?
00:45 deafferret dnewkirk: heh. i'm in it right now
00:50 dnewkirk is it more efficient to commit after each insert, or at the end of a large number of inserts?
00:51 deafferret dunno. try both?
00:52 dnewkirk ok
03:36 dnewkirk joined #bioperl
08:35 Lynx_ Is there a way to convet BLAST text output to XML/
08:35 Lynx_ ?
09:13 bag_ joined #bioperl
14:40 raela joined #bioperl
14:42 raela hey all. I have a file of 283,086 fasta contigs and 32 fasta strigs.. I want to pull out all contigs that the strings match to. I'm not too great with script, so my thought is to read them in, loop over strings with each looping over contigs to find matches
14:42 raela I assume this is horrible inefficient.. would anyone be able to point me to what I should look up to do it better?
15:59 driley joined #bioperl
16:07 melic_ joined #bioperl
16:10 wilywonka joined #bioperl
16:20 melic joined #bioperl
16:26 wilywonka joined #bioperl
16:44 melic joined #bioperl
16:47 kyanardag_ joined #bioperl
16:54 melic joined #bioperl
17:12 driley_ joined #bioperl
17:23 driley__ joined #bioperl
20:08 driley_ joined #bioperl
20:12 driley__ joined #bioperl
20:24 driley_ joined #bioperl
20:49 brandi joined #bioperl
20:51 brandi left #bioperl
21:17 kblin raela: do you need to do that once or again and again?
21:18 kblin raela: if you need to do it multiple times, turn the contigs into a blast database :)
21:22 raela kblin: well, I'm just planning this for one set of strings. I think I've figured it out for reading into arrays and using grep. it worked well with using test searches against the reads, so I'm switching it now to searching the contigs for the reads
21:25 kblin yeah, if you only need to extract matches for these 32 strings, that probably makes most sense
21:26 raela didn't take too long to work, actually.. awesome
21:26 raela I've never had any sort of object oriented programming, so I tend to overabuse loops. well, it worked out okay, so guess it's not too bad
21:29 kblin I'm not convinced that a task like "for all these contigs, check if they contain these strings" is a task you need OOP for
21:29 raela maybe not, but I know whenever I asked for R help, I'd be told I use loops too much
21:30 kblin :)
21:43 * deafferret waves
21:44 bag_ joined #bioperl
21:51 driley joined #bioperl
21:51 driley joined #bioperl
21:52 driley_ joined #bioperl
21:54 CIA-95 biome: Chris Fields cleanup_roles * r4d058b0 / (6 files in 4 dirs): more rearrangement; need to simplify SF - http://bit.ly/9vMubU
21:54 CIA-95 biome: Chris Fields cleanup_roles * r5e4668d / (MANIFEST MANIFEST.SKIP): update MANIFEST, MANIFEST.SKIP to skip unimplemented or bad tests - http://bit.ly/aXSyZf
21:58 CIA-95 biome: Chris Fields cleanup_roles * r1e0e52c / .gitignore : update .gitignore - http://bit.ly/aQAUiO
22:14 CIA-95 biome: Chris Fields master * rfb6defd / MANIFEST : update MANIFEST - http://bit.ly/cDm8u0
22:38 brandi joined #bioperl
22:38 brandi left #bioperl

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary