- python 3.0 or newer
- The following python packages installed:
sh,argparse,pandas. These can be installed using pip:
pip install sh argparse pandas
A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.
usage: eigenstrat_database_tools.py (-i <Input file prefix>) (-c <input ind file> | -R | -E) [-L <SAMPLE LIST> | -S Ind [-S Ind2]] [-o <OUTPUT FILE PREFIX>]
A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.
Available options:
-h, --help show this help message and exit
-g <GENO FILE NAME>, --genoFn <GENO FILE NAME>
The path to the input geno file.
-s <SNP FILE NAME>, --snpFn <SNP FILE NAME>
The path to the input snp file.
-i <IND FILE NAME>, --indFn <IND FILE NAME>
The path to the input ind file.
-o <OUTPUT FILES PREFIX>, --Output <OUTPUT FILES PREFIX>
The desired output file prefix. Three output files are created, <OUTPUT FILES PREFIX>.geno , <OUTPUT FILES PREFIX>.snp and <OUTPUT FILES PREFIX>.ind .
-C <INPUT FILE>, --Check <INPUT FILE>
Check the -i .ind file and the second .ind file for duplicate individuals. Population assignment and/or individual sex are not checked, only individual names. Names are case
sensitive.
-E, --Extract Extract the selected individuals from the EigenStrat database, creating a new set of EigenStrat files with the selected individuals only.
-R, --Remove Remove the selected individuals from the EigenStrat database, creating a new set of EigenStrat files without the selected individuals.
-L <INDIVIDUAL LIST FILE>, --SampleList <INDIVIDUAL LIST FILE>
A list of samples to be Extracted (-E) or Removed (-R) from the database. Can be a list of individual names (1 per line), or the output of duplicate check (-C). Required with -E
or -R. Mutually exclusive with -S.
-S <INDIVIDUAL>, --Sample <INDIVIDUAL>
A samples to be Extracted (-E) or Removed (-R) from the database. Can be called multiple times. Required with -E or -R. Mutually exclusive with -L.
-v, --version Print the version and exit.
A tool to calculate the numbered of covered and total reads for each individual in an EigenStrat dataset.
usage: eigenstrat_snp_coverage.py (-i <Input file prefix>) [-s <Input file suffix>] [-o <Output filepath>] [-j | --json]
A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.
Available options:
-h, --help show this help message and exit
-g <GENO FILE NAME>, --genoFn <GENO FILE NAME>
The path to the input geno file.
-s <SNP FILE NAME>, --snpFn <SNP FILE NAME>
The path to the input snp file.
-i <IND FILE NAME>, --indFn <IND FILE NAME>
The path to the input ind file.
-o <OUTPUT FILEPATH>, --Output <OUTPUT FILEPATH>
The filepath where the output table should be saved. Omit to print to stdout.
-j <JSON OUTPUT FILEPATH>, --json <JSON OUTPUT FILEPATH>
Create additional json formatted output file named <JSON OUTPUT FILEPATH> .
-v, --version Print the version and exit.
A tool to rename the SNPs in an EigenStrat snp file based on a reference EigenStrat or plink snp file. Uses the genetic coordinate of SNPs to determine identity.
usage: rename_snps.py (-i <INPUT .SNP FILE>) (-n <NAMED SNP FILE>) [-f <NAMED FILE FORMAT>]
Rename the SNPs in an eigenstrat snp file based on a reference eigenstrat or plink snp file. Uses the genetic coordinate of SNPs to determine identity.
Available options:
-h, --help show this help message and exit
-i <INPUT .SNP FILE>, --Input <INPUT .SNP FILE>
The input snp file.
-n <NAMED SNP FILE>, --Name_file <NAMED SNP FILE>
An Eigenstrat or plink formatted snp file with the desired SNP names.
-f <NAMED FILE FORMAT>, --Format <NAMED FILE FORMAT>
The format of the desired snp name file. Can be either 'EIGENSTRAT' or 'PLINK' [default: EIGENSTRAT]
-v, --version Print the version and exit.