Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-01-19

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All times shown according to UTC.

Time Nick Message
01:11 driveby_bot joined #bioperl
01:11 driveby_bot /home/svn-repositories/bioperl: r16723 (kortsch) : Make Bowtie array filespec args compatible with CommandExts
02:07 driveby_bot joined #bioperl
02:07 driveby_bot /home/svn-repositories/bioperl: r16724 (kortsch) : Fix coreq param bug
02:07 driveby_bot joined #bioperl
02:07 driveby_bot /home/svn-repositories/bioperl: r16725 (kortsch) : Bug fix - last test failure. Conflict between WrapperBase N/S and bowtie N/S.
02:07 driveby_bot joined #bioperl
02:07 driveby_bot /home/svn-repositories/bioperl: r16726 (kortsch) : Minor POD addition.
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02:41 driveby_bot /home/svn-repositories/bioperl: r16727 (kortsch) : Bug fix
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04:49 driveby_bot /home/svn-repositories/bioperl: r16728 (kortsch) : Config now in technicolor - should work with colourspace if colourseq is alpha encoded, may work if colourseq is num encoded (no CS seq to test with).
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09:20 space_agent Does anyone have experience with swissknife, a tool to parse swissprot entries?
09:29 space_agent I just try to get the Database cross references but to no avail. It shouldn't be too hard but the documentation is pretty sparse. Here is what I came up with http://codepad.org/bo8lD9KK
10:00 faceface space_agent: yes, I used that extensively
10:00 faceface hrm...
10:00 faceface lemmy find my "swissknife -> database" code for you
10:00 space_agent thanks a lot
10:00 faceface I'd like to make a 'project' from it
10:00 faceface any sugestions where?
10:02 space_agent sounds very interesting. I think it should definitively be included in bioperl.
10:02 faceface I have a git hub account aktually
10:03 faceface hrm... good idea
10:03 faceface danbolser hasn’t done anything yet
10:03 space_agent i just looked at biopython and there it is already easily usable.
10:03 faceface heh
10:04 space_agent but not to me as i have utf-8 something encoding problems
10:08 faceface I made a git project, how do I dump my files there?
10:09 faceface space_agent: never mind, where can I send a tar.gz
10:15 faceface there you go fatty, http://codepad.org/f2TRZON3
10:16 faceface db_xref       1
10:17 space_agent I'll try it right away
10:17 faceface good good :D
10:17 faceface oh... you want the mysql to go with those files?
10:17 faceface (dumps tab delimited files)
10:18 faceface iirc, there are a number of 'glytches'
10:18 faceface the schema isn't 100% trivial, but it all 'works' as in you can link anything with anything
10:20 faceface plus, it was written against an older version of swissknife
10:20 faceface hope it still works...
10:21 faceface I wonder what this does "@{[$_->text]}" ??
10:22 space_agent so i have to use it with a sql database right?
10:22 faceface no
10:23 faceface I don't like strong deps like that, so it just dumps all data to tab delimited file
10:23 faceface which you can then load into a database
10:26 faceface db_xref code starts at line 345, you can just extract that and play iwth it
10:26 space_agent I see thanks a lot, if I can be of any help testing your project or similar just tell me.
10:26 faceface I just need motivation / guideance on how to set it up
10:26 faceface but I'm happy if the code just helps you :-)
10:27 faceface I wonder why I handle FlyBase separately... flu
10:27 faceface http://codepad.org/f2TRZON3
10:27 space_agent Your code helps a lot for sure, but it would really be great to distribute it so more people can benefit from it
10:27 faceface 367
10:27 faceface right
10:28 faceface its around 8 years since I wrote it...
10:28 faceface gah... more like 10 ashtually
10:30 space_agent amazing that you still found it
10:30 faceface I have a good system... but I'm not sure if I gave you the best one though...
10:30 faceface I have a project called UniParser and a project called SproT
10:31 faceface SPTrEMBL
10:31 space_agent what are you doing there?
10:31 faceface same thing
10:32 faceface but also lots of sequence searching too... which became the 'biobasket' project
10:33 faceface I'll try to get this into GIT late next week.
10:34 space_agent tell me when it is out I am curious to take a look at it.
10:34 faceface er... its what you have
10:34 faceface mostly
10:35 faceface some scripts for downloading, and the DB schema too
10:35 faceface but not much more
10:35 faceface some READMEs
10:35 space_agent it is already quite a lot, at least in my view
10:36 faceface I think the plan was to write a paper, but that was before I got hooked on 'community peer recognition' ;-)
10:36 faceface I can dump the tar.gz somewhere, and we can work on getting it into bioperl
10:36 faceface if you like
10:36 space_agent that sounds great
10:36 space_agent I'd really like to help
10:39 faceface http://www.compbio.dundee.ac.uk​/user/dbolser/UniParser.tar.gz
10:39 faceface cool :D
10:40 faceface lets see what rbuels and flu to tell us what to do ...
10:40 space_agent very good
10:41 faceface glad I could help
10:41 * faceface goes back to $job
10:42 space_agent Thanks again and I am looking forward for working on the project. I just have to work right now but I'll be around
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14:07 flu faceface, what is your question?
15:25 deafferret o@.   .. .. ..o
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16:42 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient.  Paste to http://codepad.org/.
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22:37 deafferret oh dear. Bio::BroodComb has been Warnocked
22:43 rbuels what's that
22:45 deafferret http://en.wikipedia.org/wiki/Warnock%27s_Dilemma
22:45 deafferret patience FAIL   :)
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