Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-07-21

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

All times shown according to UTC.

Time Nick Message
01:45 svaksha left #bioperl
01:51 svaksha joined #bioperl
06:06 CIA-72 bioperl-live: Florent Angly master * r1681f9f / (5 files in 3 dirs): Fixed a bug in Bio::Seq::Meta* modules that prevented objects without meta information to be reverse-complemented - https://github.com/bioperl/bioperl-live/comm​it/1681f9f54f836943fd370737f049afb4ef59f3c0
09:06 svaksha left #bioperl
09:06 svaksha joined #bioperl
10:33 carandraug joined #bioperl
11:15 carandraug I made the changes I mentioned 2 days ago, changing the name of the sripts to have bp_ as well as fix their documentation. Could someone take a look at it? I made a pull request on github
14:36 jhannah I don't really bio* anymore, so I probably shouldn't
14:36 jhannah did you try emailing bioperl-l?
14:39 ank joined #bioperl
15:58 ank left #bioperl
15:58 ank joined #bioperl
16:11 sv40Tantigen joined #bioperl
16:11 sv40Tantigen hey everyone who knows how to get the genome sequence from a genbank file?
16:11 sv40Tantigen usign bio:::seqIO
16:21 carandraug sv40Tantigen, what do you mean get the genome sequence? The DNA sequence on the file?
16:21 sv40Tantigen yeah at the bottom under ORIGIN
16:26 carandraug sv40Tantigen, http://www.bioperl.org/wiki/HOWTO:Beginners you'll want the seq method once you get the sequence object
16:26 sv40Tantigen i would if seqIo was returning a seq object
16:27 sv40Tantigen but it returns a Bio::Seq::RichSeq
16:27 sv40Tantigen since im dealing with genbank file
16:30 jhannah a Bio::Seq::RickSeq object ISA Bio::Seq object
16:31 carandraug sv40Tantigen, The next_seq method should read data using the $self->_readline method as all Bio::SeqIO modules inherit from Bio::Root::IO. This method should return a new Bio::PrimarySeqI object. If the file or stream contains more than one sequence then repeated calls to next_seq should return a new sequence until the end of the stream, when an undefined value should be returned. If the sequence data is rich, meaning it contains featu
16:31 carandraug res and annotations then Bio::SeqI or Bio::Seq::RichSeqI objects should be returned.
16:32 carandraug sv40Tantigen, but the methods to use are the same
16:32 sv40Tantigen i mean i tried to use the seq function and it didn't work giving the error can't using this function on a Bio::Seq::RichSeq
16:33 jhannah show us your code and errors  gist.github.com
16:34 sv40Tantigen alright ill remake it bb in a second
16:38 sv40Tantigen lol just crashed my terminal though it looks like your right I printed the sequence, though I'm going to try and recreate my error
16:45 sv40Tantigen hmm i guess i misinterpreted my error because its working now.
16:45 sv40Tantigen Thanks everyone
17:03 sv40Tantigen left #bioperl
17:36 jhannah :)   yup, that happens to me most of the time too
17:58 isabellf_1 joined #bioperl
17:58 isabellf_1 left #bioperl
18:01 ank left #bioperl
18:01 ank joined #bioperl
18:07 ank left #bioperl
18:08 ank joined #bioperl
18:16 ank left #bioperl
18:16 ank joined #bioperl
18:29 ank left #bioperl
18:39 ende joined #bioperl
18:44 ende left #bioperl
18:50 ende joined #bioperl
18:56 ende left #bioperl
19:29 dnewkirk joined #bioperl
21:47 carandraug left #bioperl
22:58 tiago left #bioperl

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