pyGenClean.HeteroHap package

For more information about how to use this module, refer to the Heterozygous Haploid Module.

Module contents

Submodules

pyGenClean.HeteroHap.remove_heterozygous_haploid module

exception pyGenClean.HeteroHap.remove_heterozygous_haploid.ProgramError(msg)[source]

Bases: exceptions.Exception

An Exception raised in case of a problem.

Parameters:msg (str) – the message to print to the user before exiting.
pyGenClean.HeteroHap.remove_heterozygous_haploid.checkArgs(args)[source]

Checks the arguments and options.

Parameters:args (argparse.Namespace) – a an object containing the options of the program.
Returns:True if everything was OK.

If there is a problem with an option, an exception is raised using the ProgramError class, a message is printed to the sys.stderr and the program exists with code 1.

pyGenClean.HeteroHap.remove_heterozygous_haploid.main(argString=None)[source]

The main function of this module.

Parameters:argString (list) – the options.
pyGenClean.HeteroHap.remove_heterozygous_haploid.parseArgs(argString=None)[source]

Parses the command line options and arguments.

Parameters:argString (list) – the options.
Returns:A argparse.Namespace object created by the argparse module. It contains the values of the different options.
Options Type Description
--bfile string The input file prefix (Plink binary file).
--out string The prefix of the output files.

Note

No option check is done here (except for the one automatically done by argparse). Those need to be done elsewhere (see checkArgs()).

Sets heterozygous haploid markers to missing Plink.

Parameters:options (argparse.Namespace) – the options.
pyGenClean.HeteroHap.remove_heterozygous_haploid.safe_main()[source]

A safe version of the main function (that catches ProgramError).