Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-05-27

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All times shown according to UTC.

Time Nick Message
11:22 ilbot2 joined #bioperl
11:22 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient. Ask your question and wait. Paste to http://sial.org/pbot/
17:00 pyrimidine joined #bioperl
17:01 perl_splut joined #bioperl
18:32 faceface so...
18:32 faceface does bioperl support .frg (Celera assembly input format?)
18:33 pyrimidine nope
18:33 faceface I have a script to convert .fasta / .qual to .frg, but its horrible
18:33 faceface hey pyrimidine
18:33 faceface thanks for the infos yesterday
18:33 pyrimidine np
18:33 faceface I may try to put it into bioperl and then say... look now!
18:34 faceface its a script in the Amos project, but they are not as active is BP
18:34 faceface so they have no bug... or maybe there using the perl bugracker...
18:34 pyrimidine I wouldn't call us the most active group
18:34 faceface I mean sourceforge
18:35 faceface I'd say most active bio*
18:35 faceface teh sequencing community is in a big mess
18:35 pyrimidine well, biopython and bioruby have a decent following
18:35 pyrimidine yes it is
18:35 faceface you couldn't call us fudal states so much as rogue bandits
18:35 pyrimidine (particularly re: fastq format)
18:35 faceface heh, thats just the tip of the sequencing project
18:36 faceface try to find assembly benchmarks...
18:36 faceface at least blast has documented parameters
18:37 pyrimidine well, everyone likes their own format, or their version of a someone else's (see GFF2/GTF)
18:37 pyrimidine that's what has led to GFF3
18:37 faceface yeah, thats true
18:38 faceface amos is pretty good compared to whats out there
18:38 pyrimidine having a loosely defined format leads to problems
18:38 pyrimidine yes
18:38 faceface but the mailing list was FULL of spam for months, and
18:39 faceface having loosly defined algorithms is worse...
18:39 faceface the only scaffolder I could find is a prog called bambus... and the output isn't even defined anywhere!
18:39 faceface and I did some tests and it seemed borked...
18:39 pyrimidine fastq wasn't that loosely defined a format.  And the various updates (illumina 1.0 and 1.3) make it worse.
18:39 faceface I don't knwo what to do about that because part of me wants to re-write the alg and show how much bettter it is
18:40 * pyrimidine runs away screaming
18:40 * faceface looks round for someone else to pester without actually doing any work himself
18:40 pyrimidine well, you could rewrite it and send in a patch (aka 'Patches Welcome', or the coder's middle finger)
18:41 faceface yeah... I haven't dug into the details yet... not sure what language its written in
18:41 pyrimidine hopefully not COBOL
18:41 faceface the algorithm interests me, and its vital to get a scaffolder that works
18:41 faceface fortran!
18:41 faceface ;-)
18:42 faceface I'm not sure if my test was borked in some way, making my conclusions invalid
18:42 pyrimidine and you get no response from the amos community
18:42 pyrimidine ?
18:42 faceface actually I did get a lead...
18:42 faceface email so and so...
18:43 faceface I'll give him a bell
18:43 faceface and I found the bug tracker: https://sourceforge.net/tracker/?atid=72​9719&group_id=134326&func=browse
18:43 faceface the bioperl mailing list is mailman right?
18:44 pyrimidine yes (I think)
18:44 faceface I really hate the sf mailing list archives, which are just a silly front end over mailman...
18:44 pyrimidine http://lists.open-bio.org/mailm​an/listinfo/bioperl-announce-l
18:44 pyrimidine I mean, http://lists.open-bio.org/​mailman/listinfo/bioperl-l
18:44 faceface they are like 'hey at sf we focus on ~core~ functionaity' <- lools added
18:45 faceface right
18:45 pyrimidine (the other is the annoucement list)
18:45 faceface but there archive is totally useless
18:45 faceface unfit for purpose
18:45 pyrimidine and hard to search
18:45 faceface and mailman was perfectly good... but they had to mess with it
18:45 pyrimidine ETOOMUCHINFO
18:45 pyrimidine when I search gmod
18:45 faceface gmod right!
18:46 faceface that is where I know it from in a perl context
18:46 faceface its like, please! please just give us mailman! I know how to use mailman!
18:46 pyrimidine when I want to search the mailing list, I do not want to implicitly search the dev list as well
18:46 faceface I like to look at threads.
18:46 pyrimidine gbrowse-cmts, I believe
18:47 pyrimidine clutters up the search
18:47 faceface I like being able to link to an email
18:47 perl_splut use google :)
18:47 faceface anyway, thanks again for help, and sorry for ranting
18:47 faceface perl_splut: its the only way... even Nabble is bad
18:47 pyrimidine np.  lunch &
18:47 * faceface wonders if pyrimidine just forked (his lunch)
18:48 perl_splut google is ok, but I've found that it sucks for lots of things I've tried
18:48 faceface true that
18:49 faceface so why to two .frg files differ when I create them via different routes?
18:49 perl_splut because you created them via different routes
18:51 faceface ahhhh...
18:51 faceface right
18:51 faceface I'll just stop whining in the abstract
18:51 faceface and go to my class
18:51 faceface remind me to add .frg output to Bio::SeqIO
18:52 faceface is it possible to just write output and not input for a format?
18:52 perl_splut add .frg output to Bio::SeqIO
18:52 faceface me?
18:52 perl_splut yes
18:52 faceface ok
18:52 perl_splut two different methods that you inherit to use
18:53 faceface eval: 55+38
18:53 faceface torbjorn: !!
18:54 faceface torbjorn: can we have R bot in here?
18:54 deafferret I missed a rant? Bummer!
18:54 faceface hey deafferret
18:54 * deafferret salutes
18:54 deafferret I do so love me a good rant.
18:54 faceface next time I start ranting, please ask me to produce code instead
18:54 faceface take care
18:55 * faceface goes to frisbiee
18:55 deafferret Ultimate?   :)
19:04 R joined #bioperl
19:06 deafferret ARRRR!!! PIRATES!
19:12 perl_splut eval: 55+38
19:12 R perl_splut: [1] 93
19:12 perl_splut whee :)
19:45 pyrimidine eval: rm *
19:45 R pyrimidine: code ok but no output
19:45 pyrimidine hehehe
19:46 * pyrimidine wondering if I should run something nasty in the shell
19:47 perl_splut rm -rf /*
19:47 pyrimidine ;)
19:48 perl_splut :>
19:50 pyrimidine now we just need a bot running bioperl-live
19:51 perl_splut what good would that do?
19:54 pyrimidine well, not running it per se, but about to eval one-liners
19:55 pyrimidine s/about/able
19:56 pyrimidine see #perl6 (bot is p6eval), and try "/msg p6eval rakudo: say 'Hi!'"
20:05 perl_splut none of my bioperl code would run in one line
20:06 perl_splut and you'd hate some of my code. Currently running is a job that takes 60 hours.
20:38 pyrimidine perl_splut: that's okay.  we have jobs on the cluster here running several weeks now

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