Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-01-13

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All times shown according to UTC.

Time Nick Message
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02:22 zapanese Hi,can I make a question about Bioperl here?
02:35 leprevost no need to ask, just do it
02:36 zapanese thank you.
02:43 zapanese How do I get taxonomic information (ex.Bacteria,Firmicutes,...) for a list of accessions?
02:45 zapanese for example,input NP_623143,output Bacteria; Firmicutes; Clostridia; Thermoanaerobacterales;..
02:46 zapanese http://www.bioperl.org/wiki/HOW​TO:EUtilities_Cookbook#Get_GIs_.28as_well_as_other_informatio​n.29_for_a_list_of_accessions this example is very close,but a little different
02:47 leprevost are you familiar with the genbank file ?
02:49 zapanese Im sorry,no..
02:49 leprevost take a look at this : http://www.ncbi.nlm.nih.gov​/Sitemap/samplerecord.html
02:49 leprevost this is a sample record from the GenBank at NCBI database.
02:51 zapanese thank you.
02:51 leprevost these files have your accession number on it
02:52 leprevost now, take a look at the ORGANISM attribute...
02:52 zapanese ok
02:52 leprevost is this kind of information what you seek?
02:52 zapanese oh,yes
02:52 zapanese (I'm sorry my poor english..)
02:53 leprevost dont worry, english is not my native language either :)
02:54 leprevost so, what you have to do now is retrieve the list of files with the specific accession numbers from your list, an then parse the taxonomic information
02:54 zapanese (thank you for your kindness..)
02:55 zapanese yes
02:55 leprevost no problem :)
02:58 zapanese I don't know how to retrieve such information,all i can do is to retrieve GIs and other information I dont need..
03:00 leprevost if you have a small list you can get it on the NCBI 'by hand'. ON the other hand, if you have a big list you can use bioperl.
03:00 leprevost take a look at this tutorial: http://www.bioperl.org/wiki/HOWT​O:Beginners#The_Sequence_Object
03:01 zapanese thank you, i look
03:03 zapanese sorry I've not read even Beginners page
03:03 leprevost take some time to study this material, its very informative, you will see how to retrieve some information using bioperl.
03:06 zapanese thank you very much ,I'll take time and study this page!
03:07 leprevost ok, good luck with your study
03:08 zapanese (I think I have a big list,it contains more than 200 accession numbers..so I should study very hard!thank you)
03:09 leprevost yeah, heh, better use some code.
03:09 leprevost youre welcome
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13:25 deafferr1t rbuels: hey neat, they made a documentary of your new life in boston: http://www.youtube.com/watch?v=ixfchZ1s47Q
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20:49 CIA-67 bioperl-live: Chris Fields master * re2b0616 / (Bio/SeqUtils.pm t/SeqTools/SeqUtils.t):
20:49 CIA-67 bioperl-live: Merge pull request #31 from fschwach/master
20:49 CIA-67 bioperl-live: Adding molecular cloning methods to Bio::SeqUtils (+10 more commits...) - http://git.io/MxZvTg
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