Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-20

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All times shown according to UTC.

Time Nick Message
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16:23 deafferret ...o.
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17:11 batta hello there
17:18 * deafferret waves
17:18 rbuels batta: oh hello there!
17:19 batta hay r u using bioperl
17:19 rbuels ya i uses it
17:19 batta i had some doubts in it
17:20 batta can u help me
17:20 rbuels yes we probably can
17:21 deafferret batta: if you ask a question we may be able to help
17:22 batta in that i tried to use functions for performing pair wise alignment but i did not get the pathway and OOPs paradigm to perform dat
17:23 batta can u give me a breif hint of dat
17:24 deafferret batta: do you have any source code you can show us? Paste to http://codepad.org/
17:24 rbuels batta: have you looked at the bioperl searchIO howto?  http://www.bioperl.org/wiki/HOWTO:SearchIO
17:27 batta no currently i do not have code with me I'll certainly show u soon
17:31 batta does searchIO helps me in performing pairwise alignment
17:34 deafferret I'm not aware of any Perl that actually *does* alignments. There's some Smith-Waterman stuff I haven't looked at in a while, maybe that works? Often BioPerl is for processing the results of alignment, not actually performing the alignment.
17:34 deafferret use clustalw?
17:40 batta k
17:42 batta No i want the results of the alignment to be included in my perl program which takes lot of inputs
17:42 batta if i use clustalw and my program the work will be hectic rite
17:46 deafferret I don't know what "hectic rite" means
17:47 deafferret adding the results of alignment into a big perl program is easy with Bio::SearchIO
17:47 deafferret did you read the HOWTO rbuels sent you to?
17:50 batta in dat searchIO there is bl2seq it means performing alignment between 2 seq rite
17:52 deafferret yup
17:53 deafferret I tend to run bl2seq outside of BioPerl, then pull in the results file. But the standalone stuff can wrap the call to clustalw for you if you prefer
17:59 batta u mean run alignment outside like in clustallw and copy results into to a notpad and use my program to use dat results for further task
17:59 batta if i do so
18:00 perl_splut you can use clustal within bioperl via the run module that is part of Bioperl-run
18:00 batta i would need to do so for 80*80 times
18:00 batta wt
18:01 deafferret batta: um, no. I do everything in Linux, and 100% automated. Are you on Windows.
18:01 deafferret ?
18:01 batta then how can i take results from clustalw
18:01 batta until now i was i windows
18:02 deafferret batta: (for the 3rd time:) did you read the HOWTO rbuels sent you to?
18:02 batta still not worked in linux i will now onwords
18:03 deafferret I don't do anything on Windows, so I won't be able to help there. There are a couple different ways to run thousands of bl2seq runs on Linux.
18:03 rbuels batta: the general strategy you will want is to run clustalw from inside your script, then use Bio::SearchIO to parse its output
18:04 batta k i'll try to work in linux....
18:07 batta k rbuels i would have to search the serchIO ...as u said...
18:07 batta thanks for suggestions guys...... :)
18:07 deafferret glad to help   :)
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18:24 batta hay anybody there
18:25 deafferret uh, ya. you're the one that left. we're here all day  :)
18:25 batta i have chatted with others here will not it be saved
18:26 deafferret what?
18:26 batta chat history not saved
18:26 perl_splut that's up to your client to do
18:27 deafferret here's a list of IRC clients people use here: http://bioperl.org/wiki/IRC
18:27 deafferret I use irssi, which logs everything on my screens, and to files.
18:27 perl_splut so will most any IRC client. mIRC does it if you tell it to
18:27 batta k
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