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
continue
else:
#tmp = line.rstrip().split("\t")
mipName, upstream,gapfill,downstream = line.rstrip().split("\t")[0:4]
strand = "+"
mm, count = mipName.split("-")
count=int(count)
if count % 2 == 0:
strand = "-"
##based on upstream coordinate to excat seq
upStart,upStop = upstream.split("-")
downStart,downStop = downstream.split("-")
myUpSeq = nibFragger(chrom,upStart,int(upStop)-int(upStart)+1)
myDownSeq = nibFragger(chrom,downStart,int(downStop)-int(downStart)+1)
h2pos=""
h1pos=""
H1Seq=""
H2Seq=""
if strand == "+":
h2pos=upstream
h1pos=downstream
H2Seq = myUpSeq
H1Seq = myDownSeq
else:
h1pos=upstream
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
for line in open(input_file):
parts = line.rstrip().split("\t")
if line.startswith("Gene"):
continue
info("Doing " + "|".join(parts[:3]))
gene, mutation_AA, mutation_cDNA, chrome, start, end, ref, alt, gene_strand, cosmic, tumor_type = parts[
0], parts[1], parts[2], parts[3], int(parts[4]), int(
parts[5]), parts[6], parts[7], parts[8], parts[9], parts[10]
## Only works for SNP
## Situation 1: SNP_on_GF (snp in gap fill)
flank5 = nibFragger(chrome.replace("chr", ""), start - 50, 50)
flank3 = nibFragger(chrome.replace("chr", ""), end + 1, 50)
forwardSeq = flank5.lower() + "[" + ref + "/" + alt + "]" + flank3.lower()
reverseSeq = revcomp(flank3).lower() + "[" + revcomp(ref) + "/" + revcomp(
alt) + "]" + revcomp(flank5).lower()
resultStr = ""
mType = determineMutationType(ref, alt)
if mType == "SNP":
resultStr = SNP_MIP_Gap(chrome, start, end, min_hom_length,
max_hom_length, tm_min, tm_max,
gc_threshold_min, gc_threshold_max, ref, alt)
else:
print("Right now, it only supports SNP")
continue
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
output = open(output_file, "w")
output.write("hom_name\tregion_index\tchrom\tregion_start\tregion_stop\thom_start\thom_stop\tseq\tseq_tm\tgc_count\tgc_pct\tdust_scoreH1\tdust_scoreH2\tdust_pct_H1\tdust_pct_H2\thp_run\tSNPs\tSMs\n")
out_fasta = open(output_fasta, "w")
out_bed = open(output_bed, "w")
info("There are total of {} exons".format(str(len(target_regions))))
for region_index, (chrom, start, stop) in enumerate(target_regions):
#For every position in the index, design a hom - extend mip to the right
i = region_index+1
bp = str(abs(stop-start+1))
info("Finding homs on exon {} ({}-{}| {}bp)".format(str(i),str(start),str(stop),bp))
for hom_position in range(start - mip_offset - 20, stop + mip_offset):
hom_seq = nibFragger(chrom.replace("chr",""), hom_position, 35)
opt_seq, opt_tm = optimize_seq(hom_seq)
gc_count = opt_seq.count("C") + opt_seq.count("G")
gc_content = gc_count / float(len(opt_seq))
(hp_run, dust_score_H1, dust_score_H2, dust_pct_H1, dust_pct_H2) = score_dust(opt_seq)
#Disqualify homs based on thresholds
if len(opt_seq) > max_hom_length or len(opt_seq) < min_hom_length: continue
if opt_tm < tm_min or opt_tm > tm_max: continue
if gc_content > gc_threshold_max or gc_content < gc_threshold_min: continue
SNPs = snp_finder.local_snps(hom_position, hom_position + len(opt_seq) - 1)
SMs = snp_finder.local_sms(hom_position, hom_position + len(opt_seq) - 1)
end_position = hom_position + len(opt_seq) - 1
output.write("{}-{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{:.2f}\t{}\t{:.2f}\t{}\t{}\t{:.2f}\t{:.2f}\t{}\t{}\t{}\n".format(region_index, hom_position, region_index, chrom, start, stop, hom_position, end_position, opt_seq, opt_tm, \
gc_count, gc_content, dust_score_H1, dust_score_H2, dust_pct_H1, dust_pct_H2, hp_run, SNPs, SMs))
