Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-12-04

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All times shown according to UTC.

Time Nick Message
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01:36 KR hello
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01:37 KR I have some experience with Perl but am new to Bioperl... and have some questions regarding the eutils routines
01:38 KR specifically, how one uses the efetch tool to extract info fro the 'snp' database
01:46 KR I have a list of SNP rs#s  and would like to use utils to extract the reference allele and alternate allele, in addition to ~20nt flanking each side of each SNP.   I see there is some example code in the cookbook on how to use eutils to deal with the protein and nucleotide databases, but some example code for dealing with SNP data would be helpful
01:46 KR Thanks1!!
01:58 deafferret hmm, I don't think I've ever used eutils for SNPs....
01:59 deafferret do the docs help? can you tell me where you're looking?   :)
02:06 KR hi
02:06 KR sure can
02:06 KR so, I was looking the cookbook   http://www.bioperl.org/wiki​/HOWTO:EUtilities_Cookbook
02:07 KR and trying to apply the functions listed ot the 'snp' database
02:07 KR I had originallly installed the perl API variation tools from ensembl
02:07 KR but they do not have the most recent snp data from 1000genomes
02:08 KR the dbSNP 132 build
02:08 KR which have many of the snps on my list
02:08 KR so, I can use the commands from the api to get the data, but only for a portion of the snps....
02:08 KR I thought the eutils might be a better route, since they have the 132 data
02:10 KR if there is a better way than using eutils, I'm all ears...or eyes
02:14 deafferret hmm... this is the only part that mentions SNPs?   http://www.bioperl.org/wiki/HOWTO:​EUtilities_Cookbook#How_do_I_find_​all_the_SNPs_in_a_particular_gene.3F
02:17 KR right, pretty sparse... you can use the esummary data to get the snp summary
02:17 KR from  a few examples up
02:18 KR I don't know how to specify the particular data....
02:18 KR or if there's a better way to do it?
02:18 KR I was basically just switching the db -> 'gene'
02:18 KR to 'snp'
02:19 KR and for the ID using the rs#
02:19 KR instead of the gene name
02:27 deafferret so you are successfully retrieving the "132 data" which is what you were shooting for?
02:33 KR I can get the esummary data for the 132 SNPs... but I don't know how to use the other functions to output major and minor alleles, and also the sequence flanking the snp.
02:35 KR I want to retrieve the   SNP rs#,  5' flanking sequence 20nt,  3' flanking sequence 20nt,  Major allele,  Minor allele
02:36 KR using the rs# as the search term
02:41 deafferret hopefully somebody will show up with some experience, otherwise you might try the bioperl-l mailing list
02:42 KR cool, thanks!
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14:54 deafferret ...or not  :/
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16:10 newtobioperl hello everyone. Has anyone ever tried to install Qiime and its dependencies on Ubuntu?
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16:17 deafferret dunno what that is, sorry
16:20 * deafferret wonders if github Issues are version controlled in a cloneable repo
16:22 newtobioperl No problem deafferret
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