Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-09-15

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All times shown according to UTC.

Time Nick Message
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03:26 kudrety anybody familiar with Bio::DB::SeqFeature? i'm having a nightmire with " my $segment = $db->segment($chr, $start => $end ); ", i'm getting nothing in $segment.. however, my $seq=$db->fetch_sequence($chr, $start=>$end), works fine..
03:28 kudrety is there a trick with $db->segment ($seq_id, $start => $end) ??
03:49 kudrety i tried to choose chromosome1 as segment, and none of the chr1, Chr1, 1, CHR1 work.. http://pastebin.com/9hShWbQs
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04:40 dbolser kudrety: link to docs?
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04:41 dbolser kudrety: looks like you query a feature first
04:41 kudrety dbolser, I found a workaround by creating a new Segment object with,  $segment = Bio::DB::SeqFeature::Segment->new(​$store,$seqid,$start,$end,$strand)
04:42 dbolser ic
04:42 kudrety i can get the segment for a given feature, but i couldn't get a custom segment with known start and end coordinates..
04:43 kudrety i don't know why it does not work.. the docs say, my $segment=$db->segment($chr, $start => $stop) should work, but i couldn't get it to work..
04:46 dbolser ic
04:46 dbolser night
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10:56 Yksi Hey, Having parsed a blast output with bioperl, does anyone know a quick (ish) method of  searching a list of accession numbers to find which of those have type III secretion proteins present?
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13:04 kai ah, rats
13:04 * kai found a hmmer3 parser bug
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14:22 kai and another one
14:23 kai :(
14:25 Yksi whats up?
14:26 kai my boss keeps finding bugs in my hmmer3 parser, and I actually wanted to get home early today :)
14:26 Yksi Ahhh :/
14:29 kai I mean I'm happy someone is testing the crap out of the parser, but I'm flying to a conference tomorrow and I still need to pack :)
14:29 Yksi Ah is going to be a busy night then!
14:29 Yksi It is for me too :/
14:29 Yksi MSc project due in on Friday… failing miserably
14:35 kai uh
14:35 kai good luck. that's a bit more serious than my stuff
14:35 Yksi heh yeah :/
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14:57 kai ok, fixed the easy bug, enough for today
14:58 kai the other one will take longer, that can wait until after conference season
15:08 Yksi good :) so going home a lot later than expected?
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15:23 perl_splut so glad I'm an hourly wage slave...
15:23 perl_splut don't have to worry about being made to travel or, on most days, staying late
15:25 Yksi meanwhile I wish I had a wage of some description XD
15:26 perl_splut grad student?
15:27 Yksi Currently.. Yes… Next week.. No. Going back to do another undergrad course to change my career path as I dislike (struggle) with this area far too much
15:27 perl_splut have to do undergrad to switch majors?
15:27 perl_splut that sux
15:28 Yksi To switch to forensics yes :/
15:28 Yksi but I'm skipping first year, so its only two year course, which, isn't quite so bad
15:29 perl_splut heh. Just hope I'm never on a jury in a trial that you're an expert testifying in...
15:29 Yksi Why's that?
15:30 perl_splut because I might call you out on the stats that you present, heheh
15:31 Yksi haha yeah! except.. my dads a statistician (sp?)
15:31 perl_splut "only 1 in a million would match this" so did you find the other 5-10 people in this city alone that would have that same match?, heheh
15:31 perl_splut ahh, so lying is in your blood... got it :)
15:31 Yksi HAhahah you could say that…. stats are not a nice area to learn
15:32 perl_splut but a good way to make a living "making things up"
15:32 perl_splut lies, damn lies and statistics... :)
15:32 Yksi i'd rather earn an honest living ;)
15:33 perl_splut work for the government or for a private firm?
15:33 Yksi Well.. Actually I'd like to live.. I think my parents will kill me if i dont pass this MSc
15:33 perl_splut hahah...
15:33 Yksi i'm really struggling :/
15:33 perl_splut doing microbiology?
15:33 perl_splut or bioinformatics?
15:34 Yksi informatics
15:34 perl_splut ahh, so you already have the "lies through statistics" part down :)
15:34 Yksi I have very little results to actually do stats on :/
15:34 perl_splut ooohhh... that doesn't sound good
15:35 Yksi exactly
15:36 perl_splut most of my current time is spent creating apps that perform the "lies" on data... so that our statistician doesn't have to do the work himself, heheh
15:37 Yksi that sounds considerably less pleasant than doing the lies yourself
15:38 perl_splut yep, I'm the monkey that creates the big red button
15:38 Yksi do you enjoy it
15:38 Yksi ?
15:38 perl_splut occasionally.
15:39 Yksi but most of the time no?
15:39 perl_splut not really much of a challenge as the math is so basic and the algorithms are simple
15:40 Yksi :O
15:40 Yksi would you like to swap?
15:40 Yksi Compare genomes of p. syringae instead?
15:41 perl_splut heh, I'd rather work on the app that automates that :)
15:41 Yksi arses
15:41 Yksi do you know of a method to search accession numbers to see if type III secretion proteins are present?
15:42 perl_splut I created one script that read in pairs of primers and did an analysis of them vs a given genome to show what segments of the genome they would amplify
15:42 perl_splut not off the top of my head
15:42 Yksi now you're just making me wish I had some form of brain *sobs*
15:42 perl_splut afraid I don't know all the various options available for eutils searches
15:43 Yksi mhmm
15:43 perl_splut took the script about 16 hours to compare 40,000 primers vs the 2 chromosomes of BMA
15:43 Yksi :O
15:43 Yksi long time!
15:44 perl_splut it was checking for 90% match between the primers and the chromosome
15:44 perl_splut thank god for PERL Regexp
15:45 Yksi my partner is a wizz at perl… takes me ages to figure it out and write it >.>
15:46 perl_splut heheh
15:46 perl_splut I'm not that fast with any language
15:46 Yksi she just says it takes time *shrugs*
15:46 perl_splut partly because I bounce around or don't use some things very often
15:46 Yksi mhmmm
15:47 perl_splut I started learning Wx and WxPerl to create GUIs
15:47 perl_splut had been doing either Perl/Tk or RealBasic for the GUIs previously
15:51 perl_splut I also have an app that searches both the USPTO and WIPO patents/applications for keywords. You can then subsearch those patents for words near each other which normally isn't possible, heheh
15:51 Yksi bloody geeks :P
15:52 perl_splut you say that like it's a bad thing, heheh
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15:52 Yksi it's a frustrating thing sometimes thats all
15:52 deafferret ..o.Oo..   .
15:53 Yksi my partners a bloody nightmare with her BSD and encryption and tunnelling and terminals all the time terminal this and terminal that *brainmelt*
15:54 perl_splut a female geek? no such thing...
15:55 Yksi yes there is...
15:55 Yksi i'm dating her
15:55 perl_splut nope. not possible... heheh
15:56 Yksi she's been writing an ipv6 tunnel or something for one of her web servers today im completely bamboozled by it al
15:56 perl_splut heheh
15:57 Yksi she goes ranting on that the encryption on the current tunnel setup (ipv4?) isn't high enough for what she wants to use it for (connecting to blue square remotely so she doesn't have to go into the office - or something along those lines)
15:58 perl_splut ipv4 or ipv6 don't have anything about encryption in them
15:58 Yksi then she's totally bamboozled me.. she was rabbiting on about encryption earlier
15:59 perl_splut heheh
15:59 Yksi see what i mean! she just goes on and on and on with coding and stuff and im lost
15:59 perl_splut you can encrypt the data being transported, but that isn't something that ipv4 or ipv6 devices care about
16:00 Yksi ''ipv6 tunnel is also encrypted like ipv4 tunnel, upto hazel'' (hazel being one of two servers)
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