from . import configuration as conf
from .tools import UsefulFunctions as uf
[docs]class Sequence_modifiers(object) :
"""Abtract Class. All sequence must inherit from me"""
def __init__(self, sources = {}) :
self.sources = sources
[docs] def addSource(self, name, snp) :
"Optional, you can keep a dict that records the polymorphims that were mixed together to make self. They are stored into self.sources"
self.sources[name] = snp
[docs]class SequenceSNP(Sequence_modifiers) :
"""Represents a SNP to be applied to the sequence"""
def __init__(self, alleles, sources = {}) :
Sequence_modifiers.__init__(self, sources)
if type(alleles) is list :
self.alleles = uf.encodePolymorphicNucleotide(''.join(alleles))
else :
self.alleles = uf.encodePolymorphicNucleotide(alleles)
[docs]class SequenceInsert(Sequence_modifiers) :
"""Represents an Insertion to be applied to the sequence"""
def __init__(self, bases, sources = {}, ref = '-') :
Sequence_modifiers.__init__(self, sources)
self.bases = bases
self.offset = 0
# Allow to use format like C/CCTGGAA(dbSNP) or CCT/CCTGGAA(samtools)
if ref != '-':
if ref == bases[:len(ref)]:
self.offset = len(ref)
self.bases = self.bases[self.offset:]
#-1 because if the insertion are after the last nuc we go out of table
self.offset -= 1
else:
raise NotImplemented("This format of Insetion is not accepted. Please change your format, or implement your format in pyGeno.")
[docs]class SequenceDel(Sequence_modifiers) :
"""Represents a Deletion to be applied to the sequence"""
def __init__(self, length, sources = {}, ref = None, alt = '-') :
Sequence_modifiers.__init__(self, sources)
self.length = length
self.offset = 0
# Allow to use format like CCTGGAA/C(dbSNP) or CCTGGAA/CCT(samtools)
if alt != '-':
if ref is not None:
if alt == ref[:len(alt)]:
self.offset = len(alt)
self.length = self.length - len(alt)
else:
raise NotImplemented("This format of Deletion is not accepted. Please change your format, or implement your format in pyGeno.")
else:
raise Exception("You need to add a ref sequence in your call of SequenceDel. Or implement your format in pyGeno.")
[docs]class SNPFilter(object) :
"""Abtract Class. All filters must inherit from me"""
def __init__(self) :
pass
def filter(self, chromosome, **kwargs) :
raise NotImplemented("Must be implemented in child")
[docs]class DefaultSNPFilter(SNPFilter) :
"""
Default filtering object, does not filter anything. Doesn't apply insertions or deletions.
This is also a template that you can use for own filters. A prototype for a custom filter might be::
class MyFilter(SNPFilter) :
def __init__(self, thres) :
self.thres = thres
def filter(chromosome, SNP_Set1 = None, SNP_Set2 = None ) :
if SNP_Set1.alt is not None and (SNP_Set1.alt == SNP_Set2.alt) and SNP_Set1.Qmax_gt > self.thres :
return SequenceSNP(SNP_Set1.alt)
return None
Where SNP_Set1 and SNP_Set2 are the actual names of the snp sets supplied to the genome. In the context of the function
they represent single polymorphisms, or lists of polymorphisms, derived from thoses sets that occur at the same position.
Whatever goes on into the function is absolutely up to you, but in the end, it must return an object of one of the following classes:
* SequenceSNP
* SequenceInsert
* SequenceDel
* None
"""
def __init__(self) :
SNPFilter.__init__(self)
[docs] def filter(self, chromosome, **kwargs) :
"""The default filter mixes applied all SNPs and ignores Insertions and Deletions."""
def appendAllele(alleles, sources, snp) :
pos = snp.start
if snp.alt[0] == '-' :
pass
# print warn % ('DELETION', snpSet, snp.start, snp.chromosomeNumber)
elif snp.ref[0] == '-' :
pass
# print warn % ('INSERTION', snpSet, snp.start, snp.chromosomeNumber)
else :
sources[snpSet] = snp
alleles.append(snp.alt) #if not an indel append the polymorphism
refAllele = chromosome.refSequence[pos]
alleles.append(refAllele)
sources['ref'] = refAllele
return alleles, sources
warn = 'Warning: the default snp filter ignores indels. IGNORED %s of SNP set: %s at pos: %s of chromosome: %s'
sources = {}
alleles = []
for snpSet, data in kwargs.items() :
if type(data) is list :
for snp in data :
alleles, sources = appendAllele(alleles, sources, snp)
else :
allels, sources = appendAllele(alleles, sources, data)
#appends the refence allele to the lot
#optional we keep a record of the polymorphisms that were used during the process
return SequenceSNP(alleles, sources = sources)