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breakpoint.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
# =============================================================================
# FileName: breakpoint.py
# Desc: breakpoints
# Author: Chu Yanshuo
# Email: chu@yanshuo.name
# HomePage: http://yanshuo.name
# Version: 0.0.1
# LastChange: 2017-07-28 10:10:00
# History:
# =============================================================================
'''
from collections import Counter
import random
import copy
from utils.utils import rand_DNA
class Break:
def __init__(self):
self.chrom = ""
self.hapl_type = -1
# it seems , no need
self.hapl_idx = -1
self.position = -1
self.name = ""
self.insertStr = None
# deletion的paired position
# l
self.paired_position = -1
class BreakPoints():
"""Generate BreakPoints for SCNA
注意：
1）生成breakpoint位置时候不应与已有变异重合，即应该在available空间之中
2）生成breakpoint位置与available等现场，可以保存
3）可以额外添加变异，恢复现场，生成breakpoint
"""
def __init__(self):
"""Initialize from the variant dict."""
# 原始ref，用来生成变异序列
# 返回值不能用ref做为应用，确保ref引用始终是原始，即不能向ref赋值
# self._ref = ref
# available 空间，这个空间应该是父节点去除了变异位置之后的空间
# available候选空间在breakpoint和变异位置生成时要兼容，以防止变异重叠
# 这样插入位置前后1个bp都要去除
# 这个变量随时改变，要向该变量赋值, 作为传递变量
# self._ref_avail = ref_avail
# 当前节点的变异内容，只需要额外添加该变异
# dic value: 位置、变异长度、拷贝数、基因型、名称
# 额外添加变异， BreakPoints 从父节点继承
# self._variant_dict = variant_dict
# 现场信息
# 生成变异区间，用来生成变异位置时候，判断并且确保不出现插入重合现象
# 此处为了进行ploidy操作，结构为 {chr1:{'P':[[bp1],[bp2]], 'M':[[bp3]]}}
self.breaks_list = {}
def add_ploidy(self, chrom, hapl_type, hapl_idxes):
hic = Counter(hapl_idxes)
ploidies = []
for hi in hic.keys():
hapl_idx = int(hi)
number = hic[hi]
if self._has(chrom, hapl_type, hapl_idx):
ploidies = ploidies +\
number * [self.breaks_list[chrom][hapl_type][hapl_idx]]
if self._has(chrom, hapl_type, hapl_idx):
self.breaks_list[chrom][hapl_type] = self.breaks_list[chrom][
hapl_type] + ploidies
def _has(self, chrom, hapl_type, hapl_idx):
if chrom in self.breaks_list.keys():
if hapl_type in self.breaks_list[chrom].keys():
if hapl_idx < len(self.breaks_list[chrom][hapl_type]):
return True
else:
return False
else:
return False
else:
return False
# self.breakpoints.delete_ploidy(chrom, hapl, hapl_idxes)
def delete_ploidy(self, chrom, hapl, hapl_idxes):
self.breaks_list[chrom][hapl] = [
self.breaks_list[chrom][hapl][i]
for i in range(len(self.breaks_list[chrom][hapl]))
if i not in hapl_idxes]
def generateBPs(self, variant_positions, avail_position, noDEL_position,
ref, ploidy_status):
for chrom in variant_positions.svp_dict.keys():
# CNV
vps_CNV = filter(lambda item: item.sv_type == "CNV",
variant_positions.svp_dict[chrom])
self._generateCDupBPs(chrom, vps_CNV, avail_position,
noDEL_position, ref,
ploidy_status)
self._generateCDelBPs(chrom, vps_CNV, noDEL_position, ploidy_status)
# INSERTION
vp_INSERTION = filter(
lambda item: item.sv_type == "INSERTION",
variant_positions.svp_dict[chrom])
self._generateInsBPs(chrom, vp_INSERTION,
avail_position, ploidy_status)
# DELETION
vp_DELETION = filter(
lambda item: item.sv_type == "DELETION",
variant_positions.svp_dict[chrom])
self._generateDelsBPs(chrom, vp_DELETION, ploidy_status)
vp_INVERTION = filter(
lambda item: item.sv_type == "INVERTION",
variant_positions.svp_dict[chrom])
self._generateInvsBPs(chrom, vp_INVERTION,
ploidy_status,
ref)
vp_TANDEMDUP = filter(
lambda item: item.sv_type == "TANDEMDUP",
variant_positions.svp_dict[chrom])
self._generateTandemdupBPs(chrom, vp_TANDEMDUP, ploidy_status, ref)
vp_TRANSLOCATION = filter(
lambda item: item.sv_type == "TRANSLOCATION",
variant_positions.svp_dict[chrom])
self._generateTransBPs(chrom, vp_TRANSLOCATION, avail_position,
ploidy_status, ref)
def _generateTransBPs(self, chrom, vps, avail_position, ploidy_status, ref):
for vp in vps:
position = vp.position
length = vp.sv.length
htf = vp.sv.hapl_type_from
htt = vp.sv.hapl_type_to
hif = vp.sv.hapl_idx_from
hit = vp.sv.hapl_idx_to
bp_start = self._pairedBP("DELETION", chrom, htf, hif,
position, position+length)
bp_end = self._pairedBP("DELETION", chrom, htf, hif,
position+length, position)
self._breakAppend(ploidy_status, chrom, htf, hif, bp_start)
self._breakAppend(ploidy_status, chrom, htf, hif, bp_end)
bp = Break()
bp.chrom = vp.sv.chrom_to
bp.hapl_type = htt
bp.hapl_idx = hit
bp.position = self._getRandomPosi(bp.chrom, avail_position)
bp.name = "INSERTION"
bp.insertStr = ref[chrom][htf][hif][position-1: position+length]
self._breakAppend(ploidy_status, chrom, htt, hit, bp)
def _generateInvsBPs(self, chrom, vps, ploidy_status, ref):
for vp in vps:
hapl_type = vp.sv.hapl_type
hapl_idx = vp.sv.hapl_idx
insertStr =\
ref[chrom][hapl_type][hapl_idx][
vp.position: vp.position+vp.sv.length][::-1]
bp_start = self._pairedBP(
"INVERTION",
chrom, hapl_type, hapl_idx,
vp.position,
vp.position+vp.sv.length,
insertStr)
bp_end = self._pairedBP("INVERTION",
chrom, hapl_type, hapl_idx,
vp.position+vp.sv.length,
vp.position,
insertStr)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_start)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_end)
def _generateTandemdupBPs(self, chrom, vps, ploidy_status, ref):
for vp in vps:
hapl_type = vp.sv.hapl_type
hapl_idx = vp.sv.hapl_idx
times = vp.sv.times
insertStr =\
times * ref[chrom][hapl_type][hapl_idx][
vp.position: vp.position+vp.sv.length]
bp = Break()
bp.chrom = chrom
bp.hapl_type = hapl_type
bp.hapl_idx = hapl_idx
bp.position = vp.position+vp.sv.length
bp.name = "INSERTION"
bp.insertStr = insertStr
self._breakAppend(ploidy_status, chrom, hapl_type, hapl_idx, bp)
def _generateDelsBPs(self, chrom, vps, ploidy_status):
for vp in vps:
hapl_type = vp.sv.hapl_type
hapl_idx = vp.sv.hapl_idx
bp_start = self._pairedBP(
"DELETION",
chrom, hapl_type, hapl_idx,
vp.position,
vp.position+vp.sv.length)
bp_end = self._pairedBP("DELETION",
chrom, hapl_type, hapl_idx,
vp.position+vp.sv.length,
vp.position)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_start)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_end)
def _generateInsBPs(self, chrom, vps, avail_position, ploidy_status):
for vp in vps:
# self.length = -1
# self.hapl_type = ""
# self.hapl_idx = -1
hapl_type = vp.sv.hapl_type
hapl_idx = vp.sv.hapl_idx
length = vp.sv.length
position = vp.position
insertStr = rand_DNA(length)
bp = Break()
bp.chrom = chrom
bp.hapl_type = hapl_type
bp.hapl_idx = hapl_idx
bp.position = position
bp.name = "INSERTION"
bp.insertStr = insertStr
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp)
def generateFa(self, ref):
newFa = copy.deepcopy(ref)
for chrom in ref.keys():
if not self._bpsHasChrom(chrom):
continue
else:
for hapl_type in ref[chrom].keys():
if not self._bpsHasChromHap(chrom, hapl_type):
continue
else:
for hapl_idx in\
range(len(self.breaks_list[chrom][hapl_type])):
newFa[chrom][hapl_type][hapl_idx] =\
self._generateHapStr(chrom, hapl_type, hapl_idx,
ref)
return newFa
def _bpsHasChrom(self, chrom):
return chrom in self.breaks_list.keys()
def _bpsHasChromHap(self, chrom, hapl_type):
return self._bpsHasChrom(chrom) and hapl_type in\
self.breaks_list[chrom].keys()
def _generateHapStr(self, chrom, hapl_type, hapl_idx, ref):
hapStr = ""
bks = self.breaks_list[chrom][hapl_type][hapl_idx]
bks = sorted(bks,
key=lambda item: (item.position, item.paired_position))
posis = [0] + [bks[i].position for i in range(len(bks))] \
+ [len(ref[chrom][hapl_type][hapl_idx])]
refSegs = [ref[chrom][hapl_type][hapl_idx][posis[i]:posis[i+1]] for i in
range(len(posis) - 1)]
delStart = False
invStart = False
for i in range(len(refSegs)):
if not delStart:
hapStr = hapStr + refSegs[i]
if i < len(bks):
if bks[i].name == "DUPLICATION" or\
bks[i].name == "INSERTION" or\
bks[i].name == "TRANSLOCATION":
hapStr = hapStr + bks[i].insertStr
if bks[i].name == "DELETION":
if bks[i].position < bks[i].paired_position:
if delStart:
print "Error"
delStart = True
else:
if not delStart:
print "Error"
delStart = False
if bks[i].name == "INVERTION":
if bks[i].position < bks[i].paired_position:
if invStart:
print "Error"
invStart = True
else:
hapStr = hapStr + bks[i].insertStr
if not invStart:
print "Error"
invStart = False
return hapStr
def _getRandomPosi(self, chrom, avail_position):
pois = -1
while True:
# 从候选位置中抽取插入位置，位置pois - 1
pois = avail_position.sample1posi(chrom)
print "pois sampled :{}".format(pois)
if avail_position.isOverlaped(chrom, pois, pois+1):
avail_position.takePosi(chrom, pois, pois+1)
break
else:
continue
return pois
def _getRandomInvalPosi(self, chrom, length, avail_position):
pois = -1
while True:
# 从候选位置中抽取插入位置，位置pois
pois = avail_position.sample1posi(chrom)
print "pois sampled :{}".format(pois)
if avail_position.isOverlaped(chrom, pois, pois+length):
avail_position.takePosi(chrom, pois, pois+length)
break
else:
continue
return pois
def _generateCDupBPs(self, chrom, vps, avail_position, noDEL_position,
ref, ploidy_status):
"""
生成duplication copy
"""
# 此时的ref是经过了ploidy和snv之后的，以便于生成cnv
# dic value: 位置、变异长度、拷贝数、基因型、名称
# 注意生成多重ploidy的情况
psc = Counter(ploidy_status[chrom])
for vp in vps:
genotype = vp.sv.genotype
if genotype == "NONE":
continue
else:
noDEL_position.addRange(chrom, vp.position,
vp.position+vp.sv.length)
genoCounter = Counter(genotype)
hap_set_genoc = set(genoCounter.keys())
hap_set_plosc = set(psc.keys())
for genoHap in hap_set_genoc & hap_set_plosc:
for copy_i in range(genoCounter[genoHap] -
psc[genoHap]):
bp = Break()
bp.chrom = chrom
bp.hapl_type = random.sample(['P', 'M'], 1)[0]
bp.hapl_idx = random.sample(
range(len(ref[chrom][bp.hapl_type])), 1)[0]
bp.position = self._getRandomPosi(
chrom, avail_position)
bp.name = "DUPLICATION"
hapi = random.sample(range(psc[genoHap]), 1)[0]
bp.insertStr = ref[chrom][genoHap][hapi][
vp.position:vp.position+vp.sv.length]
self._breakAppend(ploidy_status, chrom,
bp.hapl_type, bp.hapl_idx, bp)
def _breakAppend(self, ploidy_status, chrom, hapl_type, hapl_idx, bp):
# 此处为了进行ploidy操作，结构为 {chr1:{'P':[[bp1],[bp2]], 'M':[[bp3]]}}
psc = Counter(ploidy_status[chrom])
if chrom not in self.breaks_list.keys():
self.breaks_list[chrom] = {}
for hap_key in psc.keys():
self.breaks_list[chrom][hap_key] = []
for i in range(psc[hap_key]):
self.breaks_list[chrom][hap_key].append([])
else:
if hapl_type not in self.breaks_list[chrom].keys():
self.breaks_list[chrom][hapl_type] = []
for i in range(psc[hapl_type]):
self.breaks_list[chrom][hapl_type].append([])
else:
if hapl_idx not in range(
len(self.breaks_list[chrom][hapl_type])):
for i in range(hapl_idx -
len(self.breaks_list[chrom][hapl_type]) + 1):
self.breaks_list[chrom][hapl_type].append([])
self.breaks_list[chrom][hapl_type][hapl_idx].append(bp)
def _generateCDelBPs(self, chrom, vps, noDEL_position, ploidy_status):
""" 生成deletion的breakpoints
:returns: TODO
"""
# dic value: 位置、变异长度、拷贝数、基因型、名称
psc = Counter(ploidy_status[chrom])
for vp in vps:
genotype = vp.sv.genotype
if genotype == "NONE":
# 每一个单体都要形成一对del bp
for hapl_type in psc.keys():
for hapl_idx in range(psc[hapl_type]):
bp_start = self._pairedBP("DELETION",
chrom, hapl_type, hapl_idx,
vp.position,
vp.position+vp.sv.length)
bp_end = self._pairedBP("DELETION",
chrom, hapl_type, hapl_idx,
vp.position+vp.sv.length,
vp.position)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_start)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_end)
else:
genoCounter = Counter(genotype)
# 只要出现与ploidy状态，减少的位置就要写入deletion
# 出现纯合时候, No key
if len(genoCounter.keys()) < len(psc.keys()):
for hapl_type in set(psc.keys())-set(genoCounter.keys()):
for hapl_idx in range(psc[hapl_type]):
bp_start = self._pairedBP("DELETION",
chrom, hapl_type,
hapl_idx,
vp.position,
vp.position+vp.sv.length)
bp_end = self._pairedBP("DELETION",
chrom, hapl_type, hapl_idx,
vp.position+vp.sv.length,
vp.position)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_start)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_end)
for hapl_type in genoCounter.keys():
del_cp_num = psc[hapl_type] - genoCounter[hapl_type]
if del_cp_num <= 0:
continue
else:
del_cp_indexes = random.sample(
range(psc[hapl_type]), del_cp_num)
for hapl_idx in del_cp_indexes:
bp_start = self._pairedBP("DELETION",
chrom, hapl_type,
hapl_idx,
vp.position,
vp.position+vp.sv.length)
bp_end = self._pairedBP("DELETION",
chrom, hapl_type, hapl_idx,
vp.position+vp.sv.length,
vp.position)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_start)
self._breakAppend(ploidy_status, chrom,
hapl_type, hapl_idx, bp_end)
def _pairedBP(
self,
name,
chrom,
hapl_type,
hapl_idx,
position,
paired_position, insertStr=None):
"""TODO: Docstring for _generateBPdeletion.
:arg1: TODO
:returns: TODO
"""
bp = Break()
bp.name = name
bp.chrom = chrom
bp.hapl_type = hapl_type
bp.hapl_idx = hapl_idx
bp.position = position
bp.paired_position = paired_position
bp.insertStr = insertStr
return bp