Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-08-09

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

All times shown according to UTC.

Time Nick Message
02:42 sheenams joined #bioperl
03:52 tiago joined #bioperl
04:05 zenman_ joined #bioperl
04:23 zenman__ joined #bioperl
04:46 zenman joined #bioperl
05:19 zenman joined #bioperl
08:29 svaksha joined #bioperl
08:29 svaksha joined #bioperl
13:16 j_wright joined #bioperl
13:50 flu joined #bioperl
15:24 jessicajames joined #bioperl
15:24 jessicajames where can i download some sample fasta files to test blast on?
15:24 jessicajames i'm just trying to get familiar with blast..
15:31 deafferret there's lots of test data in the bioperl repo
15:32 deafferret https://github.com/bioperl/bi​operl-live/tree/master/t/data  .fa .FASTA etc
15:37 jessicajames so fasta files have the extension .aa ?
15:38 jessicajames i'm browsing ftp.ncbi.nih.gov/blast/db/fasta
16:00 rbuels jessicajames: there isn't any widespread agreement on a file extension for fasta files
16:23 deafferret everything except .notfasta is fasta  :)
16:23 deafferret note that .notfasta2 is fasta
16:42 rbuels haha
17:06 pyrimidine_ joined #bioperl
18:06 jessicajames Okay, I'm trying to search through a protein sequence and record all occurrences of tripeptides in the sequences. What's the easiest way to do this?
18:09 pyrimidine_ jessicajames: use split with a capture, something like /(\S{3})/, and map to a hash.  You will need to offset the sequence to get all three shifts.
18:10 pyrimidine_ or, probably could use subseq for that, just have to be careful of the end of the sequence
18:10 * pyrimidine_ is suspicious....
18:10 pyrimidine_ is this a homework question?
18:10 jessicajames hmmm, i'm just so new to perl, it's hard to wrap my head around how to do this.
18:11 pyrimidine_ just have to think about it logically, then see what ops work to get what you need
18:11 pyrimidine_ split the sequence into triplets == split()
18:12 jessicajames ABCDEF will be split into: ABC, BCD, CDE, DEF
18:12 pyrimidine_ right
18:12 jessicajames oaky
18:12 jessicajames okay*
18:12 pyrimidine_ subset might be easier
18:12 pyrimidine_ *substr
18:12 pyrimidine_ perldoc -f substr
18:12 jessicajames hmm, alright, should I use any bioperl modules?
18:13 pyrimidine_ one could, to get the sequence string
18:13 pyrimidine_ but beyond that I would use simple perl
18:14 ulaek joined #bioperl
19:04 pyrimidine_ joined #bioperl
19:07 pyrimidine_ joined #bioperl
19:19 pyrimidine_ joined #bioperl
20:41 sheenams joined #bioperl
21:33 tiago joined #bioperl
21:59 zenman_ joined #bioperl
22:17 dnewkirk joined #bioperl

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