pyGenClean.PlinkUtils package¶

For more information about how to use this module, refer to the Plink Utils.

Module contents¶

pyGenClean.PlinkUtils.createRowFromPlinkSpacedOutput(line)[source]¶

Remove leading spaces and change spaces to tabs.

Param:	line: a line from a Plink’s report file.
Type:	line: str
Returns:	an array containing each field from the input line.

Plink’s output files are usually created so that they are human readable. Hence, instead of separating fields using tabulation, it uses a certain amount of spaces to create columns. Using the re module, the fields are split.

>>> line = " CHR               SNP         BP   A1      A2"
>>> createRowFromPlinkSpacedOutput(line)
['CHR', 'SNP', 'BP', 'A1', 'A2']

pyGenClean.PlinkUtils.get_plink_version()[source]¶

Gets the Plink version from the binary.

Returns:	the version of the Plink software
Return type:	str

This function uses subprocess.Popen to gather the version of the Plink binary. Since executing the software to gather the version creates an output file, it is deleted.

Warning

This function only works as long as the version is returned as | PLINK! | NNN | (where, NNN is the version), since we use regular expresion to extract the version number from the standard output of the software.

Submodules¶

pyGenClean.PlinkUtils.compare_bim module¶

exception pyGenClean.PlinkUtils.compare_bim.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.PlinkUtils.compare_bim.checkArgs(args)[source]¶

Checks the arguments and options.

Parameters:	args (argparse.Namespace) – 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.PlinkUtils.compare_bim.compareSNPs(before, after, outFileName)[source]¶

Compares two set of SNPs.

Parameters:	before (set) – the names of the markers in the `before` file. after (set) – the names of the markers in the `after` file. outFileName (str) – the name of the output file.

Finds the difference between two sets of markers, and write them in the outFileName file.

Note

A ProgramError is raised if:

There are more markers in the after set than in the before set.
Some markers that are in the after set are not in the before set.

pyGenClean.PlinkUtils.compare_bim.main()[source]¶

The main function of the module.

The purpose of this module is to find markers that were removed by Plink. When Plinks exclude some markers from binary files, there are no easy way to find the list of removed markers, except by comparing the two BIM files (before and after modification).

Here are the steps of this module:

Reads the BIM file before the modification (readBIM()).
Reads the BIM file after the modification (readBIM()).
Compares the list of markers before and after modification, and write the removed markers into a file (compareSNPs()).

Note

This module only finds marker that were removed (since adding markers to a BIM file usually includes a companion file to tell Plink which marker to add.

pyGenClean.PlinkUtils.compare_bim.parseArgs()[source]¶

Parses the command line options and arguments.

Returns:	A `argparse.Namespace` object created by the `argparse` module. It contains the values of the different options.

Options	Type	Description
`--before`	string	The name of the BIM file before modification.
`--after`	string	The name of the BIM file after modification.
`--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()).

pyGenClean.PlinkUtils.compare_bim.readBIM(fileName)[source]¶

Reads a BIM file.

Parameters:	fileName (str) – the name of the BIM file to read.
Returns:	the set of markers in the BIM file.

Reads a Plink BIM file and extract the name of the markers. There is one marker per line, and the name of the marker is in the second column. There is no header in the BIM file.

pyGenClean.PlinkUtils.compare_bim.safe_main()[source]¶: A safe version of the main function (that catches ProgramError).

pyGenClean.PlinkUtils.plot_MDS module¶

exception pyGenClean.PlinkUtils.plot_MDS.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.PlinkUtils.plot_MDS.addCustomOptions(parser)[source]¶

Adds custom options to a parser.

Parameters:	parser (argparse.parser) – the parser.

pyGenClean.PlinkUtils.plot_MDS.checkArgs(args)[source]¶

Checks the arguments and options.

Parameters:	args (argparse.Namespace) – 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.PlinkUtils.plot_MDS.extractData(fileName, populations)[source]¶

Extract the C1 and C2 columns for plotting.

Parameters:	fileName (dict) – the name of the MDS file. populations – the population of each sample in the MDS file.
Returns:	the MDS data with information about the population of each sample. The first element of the returned tuple is a tuple. The last element of the returned tuple is the list of the populations (the order is the same as in the first element). The first element of the first tuple is the C1 data, and the last element is the C2 data.

Note

If a sample in the MDS file is not in the population file, it is skip.

pyGenClean.PlinkUtils.plot_MDS.main()[source]¶

The main function of the module.

These are the steps:

Reads the population file (readPopulations()).
Extract the MDS data (extractData()).
Plots the MDS data (plotMDS()).

pyGenClean.PlinkUtils.plot_MDS.parseArgs()[source]¶

Parses the command line options and arguments.

Returns:	A `argparse.Namespace` object created by the `argparse` module. It contains the values of the different options.

Options	Type	Description
`--file`	string	The MBS file.
`--population-file`	string	A file containing population information.
`--format`	string	The output file format.
`--title`	string	The title of the MDS plot.
`--xlabel`	string	The label of the X axis.
`--ylabel`	string	The label of the Y axis.
`--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()).

pyGenClean.PlinkUtils.plot_MDS.plotMDS(data, theOrders, theLabels, theColors, theSizes, theMarkers, options)[source]¶

Plot the MDS data.

Parameters:

data (list of numpy.array) – the data to plot (MDS values).
theOrders (list) – the order of the populations to plot.
theLabels (list) – the names of populations to plot.
theColors (list) – the colors of the populations to plot.
theSizes (list) – the sizes of the markers for each population to plot.
theMarkers (list) – the type of markers for each population to plot.
options (argparse.Namespace) – the options.

pyGenClean.PlinkUtils.plot_MDS.readPopulations(inputFileName)[source]¶

Reads a population file.

Parameters:	inputFileName (str) – the name of the population file.
Returns:	a `dict` of population for each of the samples.

pyGenClean.PlinkUtils.plot_MDS.safe_main()[source]¶: A safe version of the main function (that catches ProgramError).

pyGenClean.PlinkUtils.plot_MDS_standalone module¶

exception pyGenClean.PlinkUtils.plot_MDS_standalone.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.PlinkUtils.plot_MDS_standalone.checkArgs(args)[source]¶

Checks the arguments and options.

Parameters:	args (argparse.Namespace) – 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.PlinkUtils.plot_MDS_standalone.extractData(fileName, populations, population_order, xaxis, yaxis)[source]¶

Extract the C1 and C2 columns for plotting.

Parameters:	fileName (str) – the name of the MDS file. populations (dict) – the population of each sample in the MDS file. population_order (list) – the required population order. xaxis (str) – the component to print as the X axis. yaxis (str) – the component to print as the Y axis.
Returns:	the MDS data with information about the population of each sample. The first element of the returned tuple is a tuple. The last element of the returned tuple is the list of the populations (the order is the same as in the first element). The first element of the first tuple is the C1 data, and the last element is the C2 data.

Note

If a sample in the MDS file is not in the population file, it is skip.

pyGenClean.PlinkUtils.plot_MDS_standalone.main()[source]¶

The main function of the module.

These are the steps:

Reads the population file (readPopulations()).
Extracts the MDS values (extractData()).
Plots the MDS values (plotMDS()).

pyGenClean.PlinkUtils.plot_MDS_standalone.parseArgs()[source]¶

Parses the command line options and arguments.

Returns:	A `argparse.Namespace` object created by the `argparse` module. It contains the values of the different options.

Options	Type	Description
`--file`	string	The MBS file.
`--population-file`	string	A file containing population information.
`--population-order`	string	The order to print the different populations.
`--population-colors`	string	The population point color in the plot.
`--population-sizes`	string	The population point size in the plot.
`--population-markers`	string	The population point marker in the plot.
`--population-alpha`	string	The population alpha value in the plot.
`--format`	string	The output file format.
`--title`	string	The title of the MDS plot.
`--xaxis`	string	The component to print on the X axis.
`--xlabel`	string	The label of the X axis.
`--yaxis`	string	The component to print on the Y axis.
`--ylabel`	string	The label of the Y axis.
`--legend-position`	string	The position of the legend.
`--legend-size`	int	The size of the legend text.
`--legend-ncol`	int	The number of columns for the legend.
`--legend-alpha`	float	The alpha value of the legend.
`--title-fontsize`	int	The font size of the title.
`--label-fontsize`	int	The font size of the X and Y labels.
`--axis-fontsize`	int	The font size of the X and Y axis.
`--adjust-left`	float	Adjust the left margin.
`--adjust-right`	float	Adjust the right margin.
`--adjust-top`	float	Adjust the top margin.
`--adjust-bottom`	float	Adjust the bottom margin.
`--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()).

pyGenClean.PlinkUtils.plot_MDS_standalone.plotMDS(data, theOrders, theLabels, theColors, theAlphas, theSizes, theMarkers, options)[source]¶

Plot the MDS data.

Parameters:

data (list of numpy.array) – the data to plot (MDS values).
theOrders (list) – the order of the populations to plot.
theLabels (list) – the names of the populations to plot.
theColors (list) – the colors of the populations to plot.
theAlphas (list) – the alpha value for the populations to plot.
theSizes (list) – the sizes of the markers for each population to plot.
theMarkers (list) – the type of marker for each population to plot.
options (argparse.Namespace) – the options.

pyGenClean.PlinkUtils.plot_MDS_standalone.readPopulations(inputFileName, requiredPopulation)[source]¶

Reads a population file.

Parameters:	inputFileName (str) – the name of the population file. requiredPopulation (list) – the required population.
Returns:	a `dict` containing the population of each samples.

pyGenClean.PlinkUtils.plot_MDS_standalone.safe_main()[source]¶: A safe version of the main function (that catches ProgramError).

pyGenClean.PlinkUtils.subset_data module¶

exception pyGenClean.PlinkUtils.subset_data.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.PlinkUtils.subset_data.checkArgs(args)[source]¶

Checks the arguments and options.

Parameters:	args (argparse.Namespace) – 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.

Note

Only one operation for markers and one operation for samples can be done at a time. Hence, one of --exclude or --extract can be done for markers, and one of --remove or --keep can be done for samples.

pyGenClean.PlinkUtils.subset_data.main(argString=None)[source]¶

The main function of the modile.

Parameters:	argString (list) – the options.

Here are the steps:

Prints the options.
Subset the data (subset_data()).

Note

The type of the output files are determined by the type of the input files (e.g. if the input files are binary files, so will be the output ones).

pyGenClean.PlinkUtils.subset_data.parseArgs(argString=None)[source]¶

Parses the command line options and arguments.

Parameters:	argString (list) – the parameters.
Returns:	A `argparse.Namespace` object created by the `argparse` module. It contains the values of the different options.

Options	Type	Description
`--ifile`	string	The input file prefix.
`--is-bfile`	bool	The input file is a bfile
`--is-tfile`	bool	The input file is a tfile
`--is-file`	bool	The input file is a file
`--exclude`	string	A file containing SNPs to exclude from the data set.
`--extract`	string	A file containing SNPs to extract from the data set.
`--remove`	string	A file containing samples (FID and IID) to remove from the data set.
`--keep`	string	A file containing samples (FID and IID) to keep from the data set.
`--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()).

pyGenClean.PlinkUtils.subset_data.runCommand(command)[source]¶

Runs a command.

Parameters:	command (list) – the command to run.

If there is a problem, a ProgramError is raised.

pyGenClean.PlinkUtils.subset_data.safe_main()[source]¶: A safe version of the main function (that catches ProgramError).

pyGenClean.PlinkUtils.subset_data.subset_data(options)[source]¶

Subset the data.

Parameters:	options (argparse.Namespace) – the options.

Subset the data using either --exclude or --extract``for markers or ``--remove or keep for samples.

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pyGenClean.PlinkUtils package¶

Module contents¶

Submodules¶

pyGenClean.PlinkUtils.compare_bim module¶

pyGenClean.PlinkUtils.plot_MDS module¶

pyGenClean.PlinkUtils.plot_MDS_standalone module¶

pyGenClean.PlinkUtils.subset_data module¶