Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-10-20

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All times shown according to UTC.

Time Nick Message
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15:04 CEP Hello
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15:06 CEP I am trying to map two nucleotide data sets what module or program do I use
15:13 deafferret define "map"
15:23 kai the X marks the treasure, or the part where sequencing failed
15:30 deafferret :)
15:35 dbolser a2a mapper
15:35 dbolser ^^ CEP
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20:04 pyrimidine never thought I would see something more obfuscated than Bio::Locations, then I ran into BioConductor's GRanges
20:05 pyrimidine can't even frickin' easily iterate over them, GAH!
20:05 pyrimidine <rant over>
20:11 rbuels that's it.  time to reimplement bioconductor in perl!
20:13 kblin hehe
20:15 pyrimidine I do have to say, there are some very nice functional programming bits in R.  And then, there are some pretty bone-headed constructs
20:16 rbuels guy i work with was recently trying to do some graphs using Chart::Clicker, and was not liking it.
20:16 rbuels kept saying "this is so much easier in R"
20:16 pyrimidine that's true
20:18 pyrimidine easy as 'plot(x~y,...)' or similar
20:18 pyrimidine but the problem comes when you step outside simple statistical analyses
20:18 perl_splut somebody took a lot of effort to make it easier in R
20:18 pyrimidine right
20:18 pyrimidine wish that same thought was put into some of the BioC stuff
20:19 pyrimidine I think the BioC community has coalesced around a few things well (ESet, etc), but one would think they would look at prior art to work out some things
20:20 pyrimidine like Genome Ranges, for instance
20:20 perl_splut all depends on the individual programmers
20:20 perl_splut like BioPerl, they work on what they need and then move on
20:20 rbuels that's why we need parrot so badly
20:21 pyrimidine right, but that's a recognized well-acknowledged problem with bioperl
20:21 pyrimidine rbuels: 100% agree
20:22 pyrimidine just seems like they have decided to go several routes with regards to something as simple as features/ranges.  it's overly obfuscated
20:22 pyrimidine okay, <rant really over>
20:24 perl_splut heheh
20:44 kblin oh, that reminds me, I ran into another issue with the embl parser/writer..
20:45 kblin it seems like the writer likes to introduce line-breaks after - signs
20:45 kblin even if you have a string like "evalue: 1.3e-17"
20:46 rbuels lol
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20:46 kblin if you then reparse the string, the parser will replace the newline with a space
20:47 kblin leaving you with "evalue: 1.3e -17"
20:47 kblin er, 1.3e- 17 actually
20:48 kblin which doesn't parse into a floating point value too well
20:49 pyrimidine let me guess, this occurs in features, correct?
20:49 pyrimidine kblin: sorry, ^^^^
20:51 kblin yeah, I've hit it in a note to a CDS_motif, but I think the parser works pretty much the same for all of the features
20:51 pyrimidine kblin: I'm guessing the writer is trying to be smart with hyphenation
20:51 kblin yeah
20:51 kblin so I wonder if we want to parser to be similar
20:52 kblin e.g. parse foo-\nbar into foo-bar
20:52 rbuels probably you only need to tweak the regexp so that it doesn't do that if there is a digit before the '-'
20:52 rbuels well, \d\s*
20:52 rbuels that would keep it from putting a break in '3-prime' as well
20:53 rbuels pyrimidine: what do you think about that?
20:53 rbuels pyrimidine: leave that baby alone, it can stand to have poop in its drawers for a while
20:53 rbuels pyrimidine: this is serious stuff here!
20:54 pyrimidine I think that's fine (and wifey's dealing with the baby poop ATM :)
20:54 rbuels lol
20:54 kblin ok, I'll have a look at that then
20:57 pyrimidine kblin: see Bio::SeqIO::embl::P_write_line_EMBL_regex
20:57 pyrimidine kblin: and a warning, might be nastier to work this in than you think
20:58 pyrimidine (at least by looking at the code)
21:04 rbuels wow!
21:04 rbuels i just smashed a fly, and tiny live maggots squirted out of its body!
21:04 * rbuels looks up how this could be
21:05 kblin seen that before
21:05 kblin both the maggots and the _write_line_EMBL_regex
21:06 kblin icky, both of them.. especially _write_line_EMBL_regex ;)
21:06 rbuels http://www.youtube.com/watch?v=XliKJB4vru8
21:08 pyrimidine survival instinct (maggots, not _write_line_EMBL_regex)
21:08 pyrimidine _write_line_EMBL_regex is the opposite of that
21:09 rbuels apparently, some species of fly are viviparous
21:11 rbuels wow, those little maggots are pretty speedy
21:11 kblin and huge.
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