Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-06

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All times shown according to UTC.

Time Nick Message
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09:49 faceface is it me or is this channel thinning out?
09:49 faceface or maybe it really is me!
09:49 faceface anyway, any good 'sequence masking' code?
10:20 kai hm, I think it's usually about this size
10:26 faceface OK
10:27 faceface how to combine a SeqIO object with a FeatureIO ?
10:34 Jun joined #bioperl
10:40 kai faceface: er, hang on
10:42 kai it's pretty straightforward
10:45 kai iirc a FeatureIO object has next_feature()
10:46 kai you can loop over those and add that to the SeqIO object
10:46 kai $seq->add_SeqFeature($feature);
10:46 kai or the like
10:46 kai the api docs are your friend
11:10 faceface right, I found that from the api too
11:10 faceface I just wondered if there was a 'smarter' way to do it
11:10 faceface what is the protocol for submitting a new script to the library?
11:11 faceface http://bioperl.pastebin.com/WndZJXKE
11:11 faceface it needs more comments, and probably needs to be a bit more generic, but I think it's scriptworthy
11:13 faceface kai: in your solution, how do I match the sequence of the SeqIO object to the sequene of the FeatureIO object?
11:13 faceface (sorry I saw the word loop in your answer and didn't look in detail)
11:17 kai you can send the script to the mailing list, I guess
11:17 faceface ic
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12:37 faceface emailed
14:32 dnewkirk so your attempting to mask repeats.
14:32 dnewkirk *you're
14:53 faceface dnewkirk: yes
14:57 dnewkirk would be a good script to use for masking consensus sequence when looking for motifs
14:59 faceface dnewkirk: one of the things that should be configurable in the script is the name of the feature that gets masked
14:59 faceface not sure if GFF should be the only feature format... I guess it could be any valid feature carrying file that BP can parse?
15:00 faceface would it be generic to just change out the -format of the FeatureIO?
15:02 dnewkirk I imagine one would only want to mask either GFF or fasta files, but there might be other as well.
15:05 faceface dnewkirk: no, I mask a sequence based on a feature
15:05 faceface in practice I mask a fasta based on a gff
15:05 faceface but both could be changed I think
15:11 dnewkirk oh, sorry, I read that wrong
15:12 dnewkirk I haven't had my coffee yet for the day
15:12 dnewkirk :/
15:13 faceface dnewkirk: np
15:13 CIA-95 bioperl-live: Lincoln Stein master * r51c9374 / (6 files in 4 dirs): added summary mode to bio::db::gff mysql adaptor - http://bit.ly/b8Pq66
15:13 faceface want to work on the script?
15:13 faceface Lincoln who?
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15:48 * rbuels chuckles
15:48 rbuels faceface: what script do you want?  run repeatmasker on potato contigs?
15:49 rbuels faceface: this is what ITAG does: http://github.com/solgenomics/ITAG-analyses/tree/​master/lib/CXGN/ITAG/Pipeline/Analysis/repeats.pm
15:49 faceface rbuels: no
15:49 faceface oh! ty
15:50 faceface rbuels: I just sent a script to the MW, and I was asking dnewkirk if he wanted to work on it
15:50 rbuels mw?
15:50 faceface sorry ML
15:50 faceface I'm working too much on MW / SMW
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16:04 * pyrimidine joins the channel, and everyone shuts up
16:09 rbuels heh
16:14 kai hehe
16:18 rbuels jeez, we sound like beavis and butthead
16:23 pyrimidine cool
16:32 kai :)
16:32 kai of to user group meeting, tada
16:35 pyrimidine anyone else here going to BOSC?
16:35 * pyrimidine stares at rbuels
16:36 * pyrimidine taps foot
16:37 rbuels pyrimidine: unfortunately, i'm not going
16:37 rbuels pyrimidine: too much other stuff going on
16:37 rbuels :-(
16:37 pyrimidine s'okay
16:37 pyrimidine I was in the same boat last year
16:55 faceface I wish I could go to teh SMW congress
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20:06 CIA-95 bioperl-live: Lincoln Stein master * r58bde58 / (5 files in 4 dirs): added interval statistics gathering to Pg adaptor - http://bit.ly/bTvpJ2
20:06 CIA-95 bioperl-live: Lincoln Stein master * r5d9a696 / Bio/DB/GFF/Adaptor/dbi/oracle.pm : ported interval statistics to oracle adaptor, but not testedperl -cw Bio/DB/GFF/Adaptor/dbi/oracle.pmperl -cw Bio/DB/GFF/Adaptor/dbi/oracle.pm - http://bit.ly/aClDlR
21:25 spekki0 has anyone used the most recent blast+ applications from ncbi, im having a bit of trouble making a blast database from a fasta file.
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