GAllele – the genome alleles module

In this module, there are the GAllele.GAlleles class (which is the class that holds the allele types) and all the allele types to use with the supported chromosomes.

class GAllele.GAlleleList(options=None)

GAlleleList Class - The list allele type

Example:

>>> alleles = GAlleles()
>>> choices = [1,2,3,4]
>>> lst = GAlleleList(choices)
>>> alleles.add(lst)
>>> alleles[0].getRandomAllele() in lst
True

add(option)

Appends one option to the options list

Parameter:option – option to be added in the list

clear()

Removes all the allele options from the list

getRandomAllele()

Returns one random choice from the options list

remove(option)

Removes the option from list

Parameter:option – remove the option from the list

class GAllele.GAlleleRange(begin=0, end=100, real=False)

GAlleleRange Class - The range allele type

Example:

>>> ranges = GAlleleRange(0,100)
>>> ranges.getRandomAllele() >= 0 and ranges.getRandomAllele() <= 100
True

Parameters:

• begin – the begin of the range
• end – the end of the range
• real – if True, the range will be of real values

add(begin, end)

Add a new range

Parameters:

• begin – the begin of range
• end – the end of the range

clear()

Removes all ranges

getMaximum()

Return the maximum of all the ranges

Return type:the maximum value

getMinimum()

Return the minimum of all the ranges

Return type:the minimum value

getRandomAllele()

Returns one random choice between the range

getReal()

Returns True if the range is real or False if it is integer

setReal(flag=True)

Sets True if the range is real or False if is integer

Parameter:flag – True or False

class GAllele.GAlleles(allele_list=None, homogeneous=False)

GAlleles Class - The set of alleles

Example:

>>> alleles = GAlleles()
>>> choices = [1,2,3,4]
>>> lst = GAlleleList(choices)
>>> alleles.add(lst)
>>> alleles[0].getRandomAllele() in lst
True

Parameters:

• allele_list – the list of alleles
• homogeneous – if is True, all the alleles will be use only the first added

add(allele)

Appends one allele to the alleles list

Parameter:allele – allele to be added