ONeSAMP 3.0
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ABSTRACT
ONeSAMP 3.0 computes the effective population size of genomic data sets. This program takes a file in GENEPOP format and computes five summary statistics. The software then uses linear regression based on these summary statistics to estimate of effective population size.
It is strongly recommended that users read the accompanying manuscript before applying ONeSAMP to their data.
USAGE OVERVIEW
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The system should be Linux.
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Must have R downloaded in order to run the software
You can download and set up the R environment at this link:
https://www.tutorialspoint.com/r/r_environment_setup.htm -
Python 3.8 or later is required to run the program
INSTALLATION
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Make a new ONeSAMP directory
mkdir OneSamp cd OneSamp -
Clone the repository
git clone [email protected]:AaronHong1024/OneSamp.git -
Give the Permission to the ONeSAMP file under the build directory
chmod 777 build/OneSamp
HOW TO RUN
usage: python main [--s number of trails] [--o input]
positional arguments:
input input file name
optional arguments:
--n Flag for Monomorphic loci (default: False)
--m Minimum Allele Frequency (size: 0-1)
--r Mutation Rate (size: 0-1)
--lNe Lower of Ne Range (size: 10-)
--uNe Upper of Ne Range (size: -500)
--lT Lower of Theta Range (size: 1-)
--uT Upper of Theta Range (size: -10)
--s Number of OneSamp Trials (size: 1000-50000)
--lD Lower of Duration Range (size: 2-)
--uD Upper of Duration Range (size: -8)
--i Missing data for individuals (size: 0-1)
--l Missing data for loci (size: 0-1)
Run the program
python main --s 1000 --o exampleData/genePop10Ix30L > output.txt