Eqmr-dbget

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Contents

Introduction

The eqmr-dbget program allows to query a database created by the eqmr-db program. The result of a query is stored in a plain-text file. Note that, before doing the first query, an index must be created: this index is stored into a binary file and will speed any subsequent queries.

Options

Short Long Description
--create-index create an index for fast retrieval
--qnorm Gaussian quantile normalize expression levels within each population
--allelic-dose provide genotype data as allelic dose
-d --data a previously created database (binary file with the .db extension)
-n --sample a single sample name or a sample file to extract
-p --pop the name of a population
-s --snp a single SNP name or a SNP file to extract
-g --gene a single gene name or a gene name file to extract
-p --probe a single probe name or a probe name file to extract
-i --index the index (created via --create-index)
-o --output the output stem

Outputs

For each kind of features that can be queried (snp, sample, gene and probe), the program creates a file suffixed _<feature>.txt. For example, if we use the option --snp, the program creates a file output_snp.txt where output corresponds to the value of the --output option. These files are described below.

Examples

We can access a short help with the following command:

$ eqmr-dbget --help
eqmr-dbget - version 2.1

Copyright (C) 2008,2009 Jean-Baptiste Veyrieras (University of Chicago)
eqmr-dbget comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.

--help	Display a brief help on program usage
--verbose	Output message on standard output to see what the program is doing

--create-index	Create an index for fast retrieval
--qnorm	Gaussian quantile normalize expression levels within each population
--allelic-dose	Provides genotype data as allelic dose

--data or -d	The input database file
--sample or -n	A single sample name or a sample file to extract
--pop or -p	The population name
--snp or -s	A single SNP name or a SNP file to extract
--gene or -g	A single gene name or a gene name file to extract
--probe or -p	A single probe name or a probe name file to extract
--index or -i	The fast index (created via --create-index)
--output or -i	The output stem

Before querying the database, we need to build the index:

$ eqmr-dbget -d eqmr.db --create-index -o eqmr.dbx --verbose

Then, for instance, we may want to get all the information on a given gene (output in file myquery_gene.txt):

$ eqmr-dbget -d eqmr.db -i eqmr.dbx -g ENSG00000212875 -o myquery

Alternatively, we may want information on 3 particular SNPs (output in file myquery_snp.txt):

$ cat subset_of_SNPs.txt
rs17160620
rs2905037
rs12124819
$ eqmr-dbget -d eqmr.db -i eqmr.dbx -s subset_of_SNPs.txt -o myquery

And of course, we can combine several options:

$ eqmr-dbget -d eqmr.db -i eqmr.dbx -g ENSG00000212875 -s subset_of_SNPs.txt -o myquery


See Also

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