def SNP_MIP_Gap(chrome,start,end,min_hom_length,max_hom_length,tm_min,tm_max,gc_threshold_min,gc_threshold_max,ref,alt):
returnStr=""
## New code on 1/21/2015
# SNP on the gap fill (use + for gap)
# if gap fill is 2 bases, it will do -+, +-
# if gap fill is 3 bases, it will do --+, -+-, +--
## Fetch sequences
for n in range(1,gap_num+1):
for j in range(0,n):
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length-(n-j-1),max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end+1+j,max_hom_length).lower()
upstream_list = get_seq(upstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
gapfill_W = nibFragger(chrome.replace("chr",""),start-(n-j-1),n)
tmplist= list(gapfill_W)
tmplist[n-j-1]=alt
gapfill_M = "".join(tmplist)
upstream_pos = chrome+":"+str(start-(n-j-1)-upstream_list[0][3])+"-"+str(start-(n-j-1)-1)
downstream_pos = chrome+":"+str(end+1+j)+"-"+str(end+1+j+downstream_list[0][3]-1)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_GF",GapFillBase_M=gapfill_M,GapFillBase_W=gapfill_W)
returnStr = returnStr.rstrip("\n")
returnStr+="\t"+upstream_pos+"\t"+downstream_pos+"\t"+getName(n,j)+"\n"
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_GF",GapFillBase_M=revcomp(gapfill_M),GapFillBase_W=revcomp(gapfill_W))
returnStr = returnStr.rstrip("\n")
returnStr+="\t"+upstream_pos+"\t"+downstream_pos+"\t"+getName(n,j)+"\n"
return returnStr
def MNP_MIP(chrome, start, end, min_hom_length, max_hom_length, tm_min, tm_max,
gc_threshold_min, gc_threshold_max, ref, alt):
returnStr = ""
# MNP on the H2 forward and H1 reverse
## Fetch sequences
upstream_seq = nibFragger(
chrome.replace("chr", ""), end - max_hom_length + 1,
max_hom_length).lower()
downstream_seq = nibFragger(
chrome.replace("chr", ""), end + 2, max_hom_length).lower()
gapfill = nibFragger(chrome.replace("chr", ""), end + 1, 1)
upstream_seq = replaceString(upstream_seq, alt, first=False)
upstream_list = get_seq(
upstream_seq,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=False)
downstream_list = get_seq(
downstream_seq,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=True)
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="+",
MIP_Mut_Alignment="MNP_on_H2",
GapFillBase_M=gapfill,
GapFillBase_W=gapfill)
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="-",
MIP_Mut_Alignment="MNP_on_H1",
GapFillBase_M=revcomp(gapfill),
GapFillBase_W=revcomp(gapfill))
## MNP on the H2 reverse Strand or H1 forward strand
upstream_seq = nibFragger(
chrome.replace("chr", ""), start - max_hom_length - 1,
max_hom_length).lower()
downstream_seq = nibFragger(
chrome.replace("chr", ""), start, max_hom_length).lower()
gapfill = nibFragger(chrome.replace("chr", ""), start - 1, 1)
### replace the first chracter
downstream_seq_replaced = replaceString(downstream_seq, alt, first=True)
upstream_list = get_seq(
upstream_seq,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=False)
downstream_list = get_seq(
downstream_seq_replaced,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=True)
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="-",
MIP_Mut_Alignment="MNP_on_H2",
GapFillBase_M=revcomp(gapfill),
GapFillBase_W=revcomp(gapfill))
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="+",
MIP_Mut_Alignment="MNP_on_H1",
GapFillBase_M=gapfill,
GapFillBase_W=gapfill)
## Do MNP_on_H2GF
for i in range(1, len(ref) + 1):
upstream_seq = nibFragger(
chrome.replace("chr", ""), start - max_hom_length - 1 + i,
max_hom_length).lower()
downstream_seq = nibFragger(
chrome.replace("chr", ""), start + i, max_hom_length).lower()
gapfillM = alt[i - 1]
gapfillW = ref[i - 1]
upOverlapWithMutation = i - 1
downOverlapWithMutation = len(ref) - i
if upOverlapWithMutation > 0:
upstream_seq = replaceString(
upstream_seq, alt[:i - 1], first=False)
if downOverlapWithMutation > 0:
downstream_seq = replaceString(downstream_seq, alt[i:], first=True)
upstream_list = get_seq(
upstream_seq,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=False)
downstream_list = get_seq(
downstream_seq,
MIN_LENGTH=min_hom_length,
MIN_TM=tm_min,
MAX_TM=tm_max,
GC_MIN=gc_threshold_min,
GC_MAX=gc_threshold_max,
right2left=True)
MIP_name = "MNP_on_"
if upOverlapWithMutation > 0:
MIP_name += "H2"
MIP_name += "Gap"
if downOverlapWithMutation > 0:
MIP_name += "H1"
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="+",
MIP_Mut_Alignment=MIP_name,
GapFillBase_M=gapfillM,
GapFillBase_W=gapfillW)
MIP_name = "MNP_on_"
if downOverlapWithMutation > 0:
MIP_name += "H2"
MIP_name += "Gap"
if upOverlapWithMutation > 0:
MIP_name += "H1"
returnStr += make_Hom_pairs(
upstream_list,
downstream_list,
hom_strand="-",
MIP_Mut_Alignment=MIP_name,
GapFillBase_M=revcomp(gapfillM),
GapFillBase_W=revcomp(gapfillW))
return returnStr
def SNP_MIP_original(chrome,start,end,min_hom_length,max_hom_length,tm_min,tm_max,gc_threshold_min,gc_threshold_max,ref,alt):
returnStr=""
# SNP on the gap fill
## Fetch sequences
if (re.search(r"[AT]",ref) and re.search(r"[CG]",alt)) or (re.search(r"[AT]",alt) and re.search(r"[CG]",ref)):
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length,max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end+1,max_hom_length).lower()
upstream_list = get_seq(upstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_GF",GapFillBase_M=alt,GapFillBase_W=ref)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_GF",GapFillBase_M=revcomp(alt),GapFillBase_W=revcomp(ref))
## SNP on the H2 forward strand and H1 reverse - Mutation Type
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length+1,max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end+2,max_hom_length).lower()
gapfill = nibFragger(chrome.replace("chr",""),end+1,1)
### replace the last chracter
upstream_seq_replaced=replaceString(upstream_seq,alt,first=False)
upstream_list = get_seq(upstream_seq_replaced, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_H2_M",GapFillBase_M=gapfill,GapFillBase_W=gapfill)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_H1_M",GapFillBase_M=revcomp(gapfill),GapFillBase_W=revcomp(gapfill))
## SNP on the H2 forward strand and H1 reverse - Wild Type
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length+1,max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end+2,max_hom_length).lower()
gapfill = nibFragger(chrome.replace("chr",""),end+1,1)
### replace the last chracter
upstream_seq_replaced=replaceString(upstream_seq,ref,first=False)
upstream_list = get_seq(upstream_seq_replaced, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_H2_W",GapFillBase_M=gapfill,GapFillBase_W=gapfill)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_H1_W",GapFillBase_M=revcomp(gapfill),GapFillBase_W=revcomp(gapfill))
## SNP on the H2 reverse Strand or H1 forward strand - Mutation Type
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length-1,max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end,max_hom_length).lower()
Mgapfill = nibFragger(chrome.replace("chr",""),end-1,1)
### replace the first chracter
downstream_seq_replaced=replaceString(downstream_seq,alt,first=True)
upstream_list = get_seq(upstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq_replaced, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_H2_M",GapFillBase_M=revcomp(gapfill),GapFillBase_W=revcomp(gapfill))
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_H1_M",GapFillBase_M=gapfill,GapFillBase_W=gapfill)
## SNP on the H2 reverse Strand or H1 forward strand - Wild Type
upstream_seq = nibFragger(chrome.replace("chr",""),start-max_hom_length-1,max_hom_length).lower()
downstream_seq = nibFragger(chrome.replace("chr",""),end,max_hom_length).lower()
Mgapfill = nibFragger(chrome.replace("chr",""),end-1,1)
### replace the first chracter
downstream_seq_replaced=replaceString(downstream_seq,ref,first=True)
upstream_list = get_seq(upstream_seq, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=False)
downstream_list = get_seq(downstream_seq_replaced, MIN_LENGTH = min_hom_length, MIN_TM=tm_min, MAX_TM=tm_max, GC_MIN=gc_threshold_min, GC_MAX=gc_threshold_max,right2left=True)
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="-",MIP_Mut_Alignment="SNP_on_H2_W",GapFillBase_M=revcomp(gapfill),GapFillBase_W=revcomp(gapfill))
returnStr+=make_Hom_pairs(upstream_list,downstream_list,hom_strand="+",MIP_Mut_Alignment="SNP_on_H1_W",GapFillBase_M=gapfill,GapFillBase_W=gapfill)
return returnStr
