parseargs

Argument parsing for the executable scripts in dms_tools2.

dms_tools2.parseargs.batch_bcsubampParser()

Returns argparse.ArgumentParser for dms2_batch_bcsubamp.

dms_tools2.parseargs.batch_diffselParser()

Returns argparse.ArgumentParser for dms2_batch_diffsel.

dms_tools2.parseargs.batch_fracsurviveParser()

Returns argparse.ArgumentParser for dms2_batch_fracsurvive

dms_tools2.parseargs.batch_prefsParser()

Returns argparse.ArgumentParser for dms2_batch_prefs.

dms_tools2.parseargs.bcsubampParentParser()

Parent parser for dms2_bcsubamp / dms2_batch_bcsubamp.

dms_tools2.parseargs.bcsubampParser()

Returns argparse.ArgumentParser for dms2_bcsubamp.

dms_tools2.parseargs.checkName(name, nametype)

Check if name is an allowable name.

Allowed names can contain most characters but not LaTex special characters.

Args:

name (str)

Name to check

nametype (str)

If we print an exception what do we call the parameter that failed? For instance, name or group.

Returns:

Returns True if name is an allowable name. Otherwise raises a ValueError explaining why the name is invalid.

>>> checkName('sample-1', 'name')
True

>>> checkName('sample 1', 'name')
True

>>> checkName('PGT151 - 5 nM', 'name')
True

>>> checkName('sample_1', 'name')
Traceback (most recent call last):
    ...
ValueError: name sample_1 contains following illegal characters: _

>>> checkName('sample_1', 'group')
Traceback (most recent call last):
    ...
ValueError: group sample_1 contains following illegal characters: _

dms_tools2.parseargs.diffselParentParser()

Parent parser for dms2_diffsel / dms2_batch_diffsel.

dms_tools2.parseargs.diffselParser()

Returns argparse.ArgumentParser for dms2_diffsel.

dms_tools2.parseargs.fracsurviveParentParser()

Parent parser dms2_fracsurvive / dms2_batch_fracsurvive

dms_tools2.parseargs.fracsurviveParser()

Returns argparse.ArgumentParser for dms2_fracsurvive.

dms_tools2.parseargs.logoplotParser()

Returns argparse.ArgumentParser for dms2_logoplot.

dms_tools2.parseargs.parentParser()

Returns parent parser with some common options added.

Returns:

argparse.ArgumentParser with the following arguments already added:

• --outdir

• --ncpus

• --use_existing

• -v / --version

dms_tools2.parseargs.parserDescription(description)

Augments description with program information.

Args:

description (str)

Description of program

Returns:

A string with description augmented with information on the dms_tools2 package / version.

dms_tools2.parseargs.prefsParentParser()

Parent parser for dms2_prefs / dms2_batch_prefs.

dms_tools2.parseargs.prefsParser()

Returns argparse.ArgumentParser for dms2_prefs.