def main(options):
hap = gdc.open2(options["hap"])
don = gdc.open2(options["donor"])
rec = gdc.open2(options["recipient"])
snp, ind, geno = [
open(options["out"] + x, "w") for x in [".snp", ".ind", ".geno"]
]
total_individuals = write_ind_file(rec, don, ind)
removed = {"multiallelic": 0}
for line in hap:
bits = line[:-1].split()
chr, pos = bits[0:2]
gts = bits[2:]
alleles = list(set(gts))
if len(alleles) > 2:
removed["multiallelic"] += 1
next
# Setting first allele to 0 - should check this is ok.
if len(gts) != 2 * total_individuals:
raise Exception("N.genotypes!=N.individuals T %s %s" % (chr, pos))
snp.write("\t".join(
[chr + ":" + pos, chr, "0.0", pos, alleles[0], alleles[1]]) + "\n")
for i in range(total_individuals):
this_gt = sum([g == alleles[0] for g in gts[(i * 2):(i * 2 + 2)]])
geno.write(str(this_gt))
geno.write("\n")
[x.close() for x in [hap, don, rec, snp, ind, geno]]
def main(options):
hap=gdc.open2(options["hap"])
don=gdc.open2(options["donor"])
rec=gdc.open2(options["recipient"])
snp, ind, geno = [open(options["out"]+x, "w") for x in [".snp", ".ind", ".geno"]]
total_individuals=write_ind_file(rec, don, ind)
removed={"multiallelic":0}
for line in hap:
bits=line[:-1].split()
chr,pos=bits[0:2]
gts=bits[2:]
alleles=list(set(gts))
if len(alleles)>2:
removed["multiallelic"]+=1
next
# Setting first allele to 0 - should check this is ok.
if len(gts)!=2*total_individuals:
raise Exception("N.genotypes!=N.individuals T %s %s"%(chr, pos))
snp.write("\t".join([chr+":"+pos, chr, "0.0", pos, alleles[0], alleles[1]])+"\n")
for i in range(total_individuals):
this_gt=sum([g==alleles[0] for g in gts[(i*2):(i*2+2)]])
geno.write(str(this_gt))
geno.write("\n")
[x.close() for x in [hap, don, rec, snp, ind, geno]]
def read_ms(ms_file, options):
"""
Read a ms file and return positions and haplotypes
"""
ms=gdc.open2(ms_file)
if options["length"]:
length=options["length"]
nhap=length=None
line=ms.next()
if options["macs"]:
nhap, length = [int(x) for x in line.split()[1:3]]
else: #For example, srcm with -SC abs
length=options["length"]
for line in ms:
if line.startswith("segsites:"):
npos=int(line.split()[1])
elif line.startswith("positions:"):
pos=np.array([int(length*float(p)) for p in line.split()[1:]])
if len(pos) != npos:
raise Exception("Number of positions does not match segsites")
break
haps=np.genfromtxt(ms, dtype=int, delimiter=1) #Assume the rest of the file is the haplotypes
haps=np.transpose(haps)
if haps.shape[0] != npos:
raise Exception("Number of positions doesn't match")
if nhap and haps.shape[1] != nhap:
raise Exception("Number of haplotypes doesn't match")
return length, pos, haps
def load_from_arp(arp):
"""
Parse an arp file into an internal format, returning site data, which is a
list of lists, with the sites on each chromosome, and gt data which is a
dict with infomation on the samples and genotypes.
I'm really just guessing what the structure of the file is.
"""
arp_file=gdc.open2(arp)
N_chr=-1
N_sites=-1
site_data=[]
gt_data={}
ascertained=False
for line in arp_file:
if line.startswith("#Number of independent chromosomes"):
N_chr=int(line.split()[-1])
if line.startswith("#Total number of polymorphic sites") and not ascertained:
N_sites=int(line.split()[-1])
if line.startswith("#ASCERTAINED DATA"):
ascertained=True
N_sites=-1
if line.startswith("#Number of polym. sites meeting ascertainment criterion:"):
N_sites=int(line.split()[-1])
if "polymorphic positions on chromosome" in line and not ascertained:
npos=int(line.split()[1])
chrom=int(line.split()[-1])
line=next(arp_file)
site_data.append(None)
site_data[chrom-1]=[int(x.replace(",", "")) for x in line[1:].split()]
if line.startswith("#Ascertained polymorphic positions on chromosome") and ascertained:
chrom=int(line.split()[-1])
line=next(arp_file)
npos=len(line.split())
site_data.append(None)
site_data[chrom-1]=[int(x.replace(",", "")) for x in line[1:].split()]
if "SampleName=" in line:
sname=line.split("\"")[-2]
line=arp_file.next()
ssize=int(line.split("=")[-1])
gt=np.zeros((N_sites, ssize), dtype='int')
arp_file.next() # "SampleData= {" line
for i in range(ssize):
line=arp_file.next()
gt_string=line.split()[2]
if len(gt_string)!=N_sites:
raise Exception("Wrong number of sites")
gt[:,i]=[int(int(x)>0) for x in gt_string] # converting {1,2,3}->1
gt_data[sname]={"size":ssize, "gt":gt}
if not N_chr==len(site_data):
raise Exception( "Number of chromosomes does not match site data" )
if not N_sites==sum([len(x) for x in site_data]):
raise Exception( "Total number of sites does not match" )
return site_data, gt_data
def main(options):
"""
Convert vcf to eigenstrat format (ind, snp and geno files)
"""
vcf=gdc.open2(options["vcf"])
snp, ind, geno = [open(options["out"]+x, "w") for x in [".snp", ".ind", ".geno"]]
removed={"multiallelic":0, "indel":0}
count=0
for line in vcf:
if line[:2]=="##": # Comment line
next
elif line[:6]=="#CHROM": # Header line
inds=line.split()[9:]
if options["ref"]:
ind.write(options["ref"]+"\tU\tREF\n")
for indi in inds:
if not options["indAsPop"]:
ind.write(indi+"\tU\tPOP\n")
else:
ind.write(indi+"\tU\t"+indi+"\n")
else: # data
bits=line.split()
if "," in bits[4]:
removed["indel"]+=1
continue
if len(bits[3])!=1 or len(bits[4])!=1:
removed["multiallelic"]+=1
continue
else:
if bits[2]==".":
bits[2]=bits[0]+":"+bits[1]
snp.write(" ".join([bits[2], bits[0], "0.0", bits[1], bits[3], bits[4]])+"\n")
geno_string=""
if options["ref"]:
geno_string="2"
for gt in bits[9:]:
geno_string+=decode_gt_string(gt)
geno.write(geno_string+"\n")
count+=1
[f.close for f in [ind, snp, geno]]
print "Done. Wrote "+str(count) + " sites"
print "Excluded " + str(sum(removed.values())) + " sites"
for key in removed:
print "Excluded " + str(removed[key]) + " " + key
return
def main(options):
"""
Convert vcf to eigenstrat format (ind, snp and geno files)
"""
vcf=gdc.open2(options["vcf"])
snp, ind, geno = [open(options["out"]+x, "w") for x in [".snp", ".ind", ".geno"]]
removed={"multiallelic":0, "indel":0}
count=0
for line in vcf:
if line[:2]=="##": # Comment line
next
elif line[:6]=="#CHROM": # Header line
inds=line.split()[9:]
if options["ref"]:
ind.write(options["ref"]+"\tU\tREF\n")
for indi in inds:
if not options["indAsPop"]:
ind.write(indi+"\tU\tPOP\n")
else:
ind.write(indi+"\tU\t"+indi+"\n")
else: # data
bits=line.split()
if "," in bits[4]:
removed["indel"]+=1
continue
if len(bits[3])!=1 or len(bits[4])!=1:
removed["multiallelic"]+=1
continue
else:
if bits[2]==".":
bits[2]=bits[0]+":"+bits[1]
snp.write(" ".join([bits[2], bits[0], "0.0", bits[1], bits[3], bits[4]])+"\n")
geno_string=""
if options["ref"]:
geno_string="2"
for gt in bits[9:]:
geno_string+=decode_gt_string(gt)
geno.write(geno_string+"\n")
count+=1
[f.close for f in [ind, snp, geno]]
print "Done. Wrote "+str(count) + " sites"
print "Excluded " + str(sum(removed.values())) + " sites"
for key in removed:
print "Excluded " + str(removed[key]) + " " + key
return
def read_ms(ms_file, options):
"""
Read a ms file and return positions and haplotypes
"""
ms = gdc.open2(ms_file)
if options["length"]:
length = options["length"]
nhap = length = None
line = ms.next()
if options["macs"]:
nhap, length = [int(x) for x in line.split()[1:3]]
else: #For example, srcm with -SC abs
length = options["length"]
for line in ms:
if line.startswith("segsites:"):
npos = int(line.split()[1])
elif line.startswith("positions:"):
pos = np.array([int(length * float(p)) for p in line.split()[1:]])
if len(pos) != npos:
raise Exception("Number of positions does not match segsites")
break
haps = np.genfromtxt(
ms, dtype=int,
delimiter=1) #Assume the rest of the file is the haplotypes
haps = np.transpose(haps)
if haps.shape[0] != npos:
raise Exception("Number of positions doesn't match")
if nhap and haps.shape[1] != nhap:
raise Exception("Number of haplotypes doesn't match")
return length, pos, haps
def read_macs(macs_file):
"""
Read a macs file and return positions and haplotypes
"""
macs=gdc.open2(macs_file)
line=macs.next()
nhap, length = [int(x) for x in line.split()[1:3]]
for line in macs:
if line.startswith("segsites:"):
npos=int(line.split()[1])
elif line.startswith("positions:"):
pos=np.array([int(length*float(p)) for p in line.split()[1:]])
if len(pos) != npos:
raise Exception("Number of positions does not match segsites")
break
haps=np.genfromtxt(macs, dtype=int, delimiter=1) #Assume the rest of the file is the haplotypes
haps=np.transpose(haps)
if haps.shape != (npos, nhap):
raise Exception("Genotype matrix shape doesn't match")
return length, pos, haps
def main(argv):
try:
opts, args = getopt.getopt(argv, "o:v:d:",
["output=", "vcf=", "diploid="])
except getopt.GetoptError:
sys.exit(2)
for opt, arg in opts:
if opt in ("-o", "--output"):
output_filename = arg
elif opt in ("-v", "--vcf"):
vcf_filename = arg
elif opt in ("-d", "--diploid"): # samples diploid? (True/False)
if (arg in ['1', 1, 'T', 't', 'True', 'true']):
d_flag = True
else:
d_flag = False
n_head_lines = 0
for vcfline in gdc.open2(vcf_filename):
n_head_lines += 1
line = vcfline.decode()
if line[1] != '#':
break
nlines = sum(1 for line in gdc.open2(vcf_filename)) - n_head_lines
vcf_file = gdc.open2(vcf_filename)
vcfline = next(vcf_file)
pound = vcfline.decode()[1]
while pound == '#':
vcfline = next(vcf_file)
pound = vcfline.decode()[1]
line = vcfline.decode()
output_head = ['ID', 'chr', 'pos', 'Alt', 'N', 'Fq']
with open(output_filename, 'w') as mycsv:
datawriter = csv.writer(mycsv)
datawriter.writerow(output_head)
#, quoting = csv.QUOTE_NONE
for i in range(0, nlines):
vcfline = next(vcf_file)
line = vcfline.decode()
line = line.split()
chr, pos = line[0], line[1]
chrpos = line[0] + '_' + line[1]
alt_count = 0
total = 0
for j in range(9, len(line)):
if line[j][0] == '.':
continue
else:
alt_count, total = tally(alt_count, line[j], d_flag, total)
if total == 0:
continue
else:
alt_fq = alt_count / total
row = [chrpos, chr, pos, alt_count, total, alt_fq]
datawriter.writerow(row)
mycsv.close()
def load_from_arp(arp):
"""
Parse an arp file into an internal format, returning site data, which is a
list of lists, with the sites on each chromosome, and gt data which is a
dict with infomation on the samples and genotypes.
I'm really just guessing what the structure of the file is.
"""
arp_file = gdc.open2(arp)
N_chr = -1
N_sites = -1
site_data = []
gt_data = {}
ascertained = False
for line in arp_file:
if line.startswith("#Number of independent chromosomes"):
N_chr = int(line.split()[-1])
if line.startswith(
"#Total number of polymorphic sites") and not ascertained:
N_sites = int(line.split()[-1])
if line.startswith("#ASCERTAINED DATA"):
ascertained = True
N_sites = -1
if line.startswith(
"#Number of polym. sites meeting ascertainment criterion:"):
N_sites = int(line.split()[-1])
if "polymorphic positions on chromosome" in line and not ascertained:
npos = int(line.split()[1])
chrom = int(line.split()[-1])
line = next(arp_file)
site_data.append(None)
site_data[chrom -
1] = [int(x.replace(",", "")) for x in line[1:].split()]
if line.startswith("#Ascertained polymorphic positions on chromosome"
) and ascertained:
chrom = int(line.split()[-1])
line = next(arp_file)
npos = len(line.split())
site_data.append(None)
site_data[chrom -
1] = [int(x.replace(",", "")) for x in line[1:].split()]
if "SampleName=" in line:
sname = line.split("\"")[-2]
line = arp_file.next()
ssize = int(line.split("=")[-1])
gt = np.zeros((N_sites, ssize), dtype='int')
arp_file.next() # "SampleData= {" line
for i in range(ssize):
line = arp_file.next()
gt_string = line.split()[2]
if len(gt_string) != N_sites:
raise Exception("Wrong number of sites")
gt[:, i] = [int(int(x) > 0)
for x in gt_string] # converting {1,2,3}->1
gt_data[sname] = {"size": ssize, "gt": gt}
if not N_chr == len(site_data):
raise Exception("Number of chromosomes does not match site data")
if not N_sites == sum([len(x) for x in site_data]):
raise Exception("Total number of sites does not match")
return site_data, gt_data
def output_hetfa(options):
"""
output a single hetfa
"""
ref_fa = Fasta(options["ref"])
mask = None
if options["mask"]:
mask = Fasta(options["mask"])
out = None
if options["out"]:
out = gzip.open(options["out"] + ".hetfa.fa.gz", "w")
else:
out = sys.stdout
out.write(">" + options["chrom"] + "\n")
vcf = gdc.open2(options["vcf"])
sample_idx = None
last_pos = 0
for line in vcf:
if line.startswith("##"):
continue
elif line.startswith("#"):
bits = line.split()
sample_idx = bits.index(options["sample"])
else: #data line
bits = line.split()
gt = bits[sample_idx]
pos = int(bits[1])
if pos == last_pos:
continue
ref = bits[3]
alt = bits[4]
masked = check_mask(mask, options, pos)
ref_seq = get_ref_seq(options, ref_fa, mask, last_pos, pos)
if len(ref) == 1 and len(alt) == 1 and gt[0] in [
"0", "1"
] and gt[2] in ["0", "1"
] and not masked: #This is a biallelic site
#This is the sequence from the last position to the base before the current position (note that pos is 1-based)
if options["refcheck"] and ref_fa[options["chrom"]][
pos - 1].seq != ref:
raise Exception("Reference mismatch at pos " + str(pos))
genotype = int(gt[0]) + int(gt[2])
if genotype == 0:
out.write(ref_seq + ref)
elif genotype == 1:
hetfa_code = HETFA_MAP[tuple(sorted([ref, alt]))]
out.write(ref_seq + hetfa_code)
elif genotype == 2:
out.write(ref_seq + alt)
else:
raise Exception(
"Untrapped bad genotype in haplotype 0 at pos" +
str(pos))
else: #This is either unphased or missing or multiallelic
out.write(ref_seq + "N")
last_pos = pos
#Fill in the reference at the end and terminate with newline.
tail_seq = ref_fa[options["chrom"]][last_pos:].seq
out.write(tail_seq + "\n")
def output_fastas(options):
"""
output two .fa files, one for each chromosome.
"""
ref_fa = Fasta(options["ref"])
out0 = gzip.open(options["out"] + ".0.fa.gz", "w")
out1 = gzip.open(options["out"] + ".1.fa.gz", "w")
out0.write(">" + options["chrom"] + "\n")
out1.write(">" + options["chrom"] + "\n")
mask = None
if options["mask"]:
mask = Fasta(options["mask"])
vcf = gdc.open2(options["vcf"])
sample_idx = None
last_pos = 0
for line in vcf:
if line.startswith("##"):
continue
elif line.startswith("#"):
bits = line.split()
sample_idx = bits.index(options["sample"])
else: #data line
bits = line.split()
gt = bits[sample_idx]
pos = int(bits[1])
if pos == last_pos:
continue
ref = bits[3]
alt = bits[4]
masked = check_mask(mask, options, pos)
ref_seq = get_ref_seq(options, ref_fa, mask, last_pos, pos)
if len(ref) == 1 and len(alt) == 1 and gt in [
"0|0", "1|0", "0|1", "1|1"
] and not masked: #This is a phased biallelic site
#This is the sequence from the last position to the base before the current position (note that pos is 1-based)
if options["refcheck"] and ref_fa[options["chrom"]][
pos - 1].seq != ref:
raise Exception("Reference mismatch at pos " + str(pos))
if gt[0] == "0":
out0.write(ref_seq + ref)
elif gt[0] == "1":
out0.write(ref_seq + alt)
else:
raise Exception(
"Untrapped bad genotype in haplotype 0 at pos" +
str(pos))
if gt[2] == "0":
out1.write(ref_seq + ref)
elif gt[2] == "1":
out1.write(ref_seq + alt)
else:
raise Exception(
"Untrapped bad genotype in haplotype 1 at pos" +
str(pos))
else: #This is either unphased or missing or multiallelic
out0.write(ref_seq + "N")
out1.write(ref_seq + "N")
last_pos = pos
#Fill in the reference at the end and terminate with newline.
tail_seq = ref_fa[options["chrom"]][last_pos:].seq
out0.write(tail_seq + "\n")
out1.write(tail_seq + "\n")
out0.close()
out1.close()
def main(options):
"""
Iterate over the vcf and output one fasta file for each chromosome.
"""
ref_fa = Fasta(options["ref"])
out0 = gzip.open(options["out"] + ".0.fa.gz", "w")
out1 = gzip.open(options["out"] + ".1.fa.gz", "w")
out0.write(">" + options["chrom"] + "\n")
out1.write(">" + options["chrom"] + "\n")
vcf = gdc.open2(options["vcf"])
sample_idx = None
last_pos = 0
for line in vcf:
if line.startswith("##"):
continue
elif line.startswith("#"):
bits = line.split()
sample_idx = bits.index(options["sample"])
else: # data line
bits = line.split()
gt = bits[sample_idx]
pos = int(bits[1])
if pos == last_pos:
continue
ref = bits[3]
alt = bits[4]
if (
len(ref) == 1 and len(alt) == 1 and gt in ["0|0", "1|0", "0|1", "1|1"]
): # This is a phased biallelic site
# This is the sequence from the last position to the base before the current position (note that pos is 1-based)
ref_seq = ref_fa[options["chrom"]][last_pos : (pos - 1)].seq
if options["refcheck"] and ref_fa[options["chrom"]][pos - 1].seq != ref:
raise Exception("Reference mismatcah at pos " + str(pos))
if gt[0] == "0":
out0.write(ref_seq + ref)
elif gt[0] == "1":
out0.write(ref_seq + alt)
else:
raise Exception("Untrapped bad genotype in haplotype 0 at pos" + str(pos))
if gt[2] == "0":
out1.write(ref_seq + ref)
elif gt[2] == "1":
out1.write(ref_seq + alt)
else:
raise Exception("Untrapped bad genotype in haplotype 1 at pos" + str(pos))
else: # This is either unphased or missing or multiallelic
out0.write("N" * (pos - last_pos))
out1.write("N" * (pos - last_pos))
last_pos = pos
# Fill in the reference at the end and terminate with newline.
tail_seq = ref_fa[options["chrom"]][last_pos:].seq
out0.write(tail_seq + "\n")
out1.write(tail_seq + "\n")
