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qngene's Introduction

How to execute the scripts in "Export_gen_files"

gentotsv.py (Converts .gen and .sample into tsv)

python gentotsv.py -> (it takes the default sourcedir, destinationdir and sample file from config.py)

or

gentotsv.py -h[help] -t[threads] -s[sourcedir] -d[destinationdir] -f[samplefile] -> (all the parameters are optionals)

export.py (Generates individuals, visits, genotypes and phenotypes files from Advance, dbSNP and .gen/.sample data sources)

python export.py {destination_des_tsv} {ip_postgresql_server} {schema_postgresql} {owner_schema_postresql} {password_owner_schema}{import_genotypes_flag}

Ex: python export.py "/Test/output" 127.0.0.1 advancedb prognomix pass12345 Y -> . Flag "import_genotypes_flag" to Y takes only individuals from Advance DB with imputed genotypes (from .sample file) and genotypes from .gen files. Flag "import_genotypes_flag" to N takes all the invidivuals and gentoypes from Advance DB).

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qngene

Join the chat at https://gitter.im/bigdatafoundation/qngene Genetic Scalable Analytical Query Engine

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qngene's Issues

Add manual in readme

Please add a brief synopsis on how to compile / run qngene.

Also, add a quick steps to get started with IntelliJ.

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