def summary_haplotype_block(vcf, haplotype, outfile):
phased_block = defaultdict(lambda : list())
phased_block_com = defaultdict(lambda : list())
import VCF
for v in VCF.lines(vcf):
block_id = re.split(r':', v['FCM'][1])[1]
genotype = re.split(r':', v['FCM'][0])[0]
#print genotype
#print '{}\t{}\t{}'.format(v['CHROM'], v['POS'], block_id)
block_idx = '{}_{}'.format(v['CHROM'], block_id)
snp_idx = '{}:{}'.format(v['CHROM'], v['POS'])
bases = [v['REF'], v['ALT']]
hap1_10x = bases[int(genotype[0])]
haplotype_flag = -1
if haplotype.has_key(snp_idx):
if hap1_10x == haplotype[snp_idx][0]:
haplotype_flag = 0
elif hap1_10x == haplotype[snp_idx][1]:
haplotype_flag = 1
phased_block[block_idx].append(int(v['POS']))
phased_block_com[block_idx].append(haplotype_flag)
ofile = open(outfile, 'w')
for blc in phased_block.keys():
snps = len(phased_block[blc])
start = np.min(phased_block[blc])
end = np.max(phased_block[blc])
length= int(end) - int(start) + 1
hap1_n = len([i for i in phased_block_com[blc] if i == 0])
hap2_n = len([i for i in phased_block_com[blc] if i == 1])
hap0_n = len([i for i in phased_block_com[blc] if i == -1])
print >> ofile, '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}'.format(blc, snps, length, start, end, hap1_n, hap2_n, hap0_n)
ofile.close()
def check_vcf( input ):
v = VCF( input )
debug = False
print "\n".join(v.metadata)
for line in v.lines():
r = line.ref
a = line.alt_list
if len(r) > 1:
if len(a) > 1:
raise Exception("WARNING: multi-allelic change not coded for")
line1 = copy.deepcopy( line )
line2 = copy.deepcopy( line )
if len(a[0]) > 1:
if len(r) < len(a[0]): # insertion
if len(r) == 2:
line1.ref = r[1]
line1.alt = r[1]+a[0][2:]
line1.pos += 1
line2.ref = r[1]
line2.alt = a[0][1]
line2.pos += 1
if debug: print "===="
print line1
print line2
if debug: print line
elif len(a[0]) < len(r):
if len(a[0]) == 2:
line1.ref = r[1:]
line1.alt = r[1]
line1.pos += 1
line2.ref = r[1]
line2.alt = a[0][1]
line2.pos += 1
if debug: print "===="
print line1
print line2
if debug: print line
else:
print line
else:
print line
else:
print line
def sort_vcf( input, reference, output ):
contig_list = get_contig_list( reference )
print "read {} contigs".format(len(contig_list))
v = VCF( input, True ) # request index of VCF upon open
with open( output, 'w') as fd_out:
fd_out.writelines( [ line+"\n" for line in v.metadata ] )
for contig in contig_list:
print "writing entries for contig {}".format(contig)
# filter lines from vcf by contig
count = 0
if v.seek(contig) < 0:
print "skipped {} because it's not in the VCF".format( contig )
else:
for line in v.lines( True, \
lambda raw_line: VCFLine(raw_line).chr == contig ):
fd_out.write( line.line+"\n" )
count += 1
print "wrote {} entries for {}".format( count, contig )
import VCF
import cyvcf2
try:
## MUST BE A UNCOMPRESSED VCF file
finput = argv[1]
except IndexError as ie:
exit("{}\nUSAGE: $0 $vcf_file ".format(ie))
if not path.exists(finput):
msg = "ERROR: FNF {}".format(finput)
raise IOError(msg)
d = {}
for v in VCF.lines(finput):
if v['CHROM'] in d:
d[v['CHROM']].append(v['POS'])
else:
d[v['CHROM']] = [v['POS']]
with open("{}.consPos.txt".format(finput), 'wt') as of:
for key,val in d.items():
## make sure all positions are integer ; if not raise error
try:
data = [int(i) for i in val]
except ValueError as ve:
exit("ERROR: {}".format(e))
# https://stackoverflow.com/questions/2361945/detecting-consecutive-integers-in-a-list
for k, g in groupby(enumerate(data), lambda ix: ix[0] - ix[1]):
cn = list(map(itemgetter(1), g))
def summary_haplotype_block(vcf, haplotype, outfile_up, outfile_down):
phased_block = defaultdict(lambda : list())
phased_block_com = defaultdict(lambda : list())
phased_block_rank = defaultdict(lambda : int())
count = 0
import VCF
for v in VCF.lines(vcf):
block_id = re.split(r':', v['FCM'][1])[1]
genotype = re.split(r':', v['FCM'][0])[0]
#print genotype
#print '{}\t{}\t{}\t{}'.format(v['CHROM'], v['POS'], block_id, v['FCM'][0])
block_idx = '{}_{}'.format(v['CHROM'], block_id)
snp_idx = '{}:{}'.format(v['CHROM'], v['POS'])
bases = [v['REF'], v['ALT']]
hap1_10x = bases[int(genotype[0])]
haplotype_flag = -1
if haplotype.has_key(snp_idx):
if hap1_10x == haplotype[snp_idx][0]:
haplotype_flag = 0
elif hap1_10x == haplotype[snp_idx][1]:
haplotype_flag = 1
if not phased_block.has_key(block_idx):
count += 1
phased_block[block_idx].append(int(v['POS']))
phased_block_com[block_idx].append(haplotype_flag)
phased_block_rank[block_idx] = count
for blc in phased_block.keys():
chrs, blc_id = re.split(r'_', blc)
snps = len(phased_block[blc])
start = np.min(phased_block[blc])
end = np.max(phased_block[blc])
length= int(end) - int(start) + 1
hap1_n = len([i for i in phased_block_com[blc] if i == 0])
hap2_n = len([i for i in phased_block_com[blc] if i == 1])
hap0_n = len([i for i in phased_block_com[blc] if i == -1])
print '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}'.format(blc, snps, length, chrs, start, end, hap1_n, hap2_n, hap0_n)
ratio = 0.0
#try:
# ratio = np.max(float(hap1_n)/(float(hap1_n)+float(hap2_n)), float(hap2_n)/(float(hap1_n)+float(hap2_n)))
#except:
# continue
min_snp = 1
if hap1_n >= min_snp and hap1_n == snps - hap0_n:
ratio = 1
elif hap2_n >= min_snp and hap2_n == snps - hap0_n:
ratio = 1
elif hap1_n >= min_snp and hap1_n > hap2_n:
ratio = float(hap1_n)/(float(hap1_n)+float(hap2_n))
elif hap2_n >= min_snp and hap2_n > hap1_n:
ratio = float(hap2_n)/(float(hap1_n)+float(hap2_n))
print ratio
if ratio > 0.95:
color = 'gray'
hap = 3
print hap1_n, hap2_n
if hap1_n > hap2_n:
color = 'orange'
hap = 1
else:
color = 'blue'
hap = 2
print color
if phased_block_rank[blc]%2 == 1:
print >> outfile_up, '{}\t{}\t{}\t{}\t{}\t+'.format(chrs, start, end, hap, color)
else:
print >> outfile_down, '{}\t{}\t{}\t{}\t{}\t+'.format(chrs, start, end, hap, color)
def nr_sensitivity( input, sample, truth, minqual=0, misses=None, debug=False ):
print >>sys.stderr,"input={}\ntruth={}\nminqual={}".format(input,truth,minqual)
truth_vcf = VCF( truth )
eval_vcf = VCF( input )
if misses:
misses_fd = open( misses, 'w' )
found = False
for line in truth_vcf.metadata:
if line[:len("#CHROM")]=="#CHROM":
misses_fd.write( '##nr_concordance="comment={subset of '\
'missed sites created by DISCOVAR release bundle Python program '\
'nr_concordance.py}"\n')
found = True
misses_fd.write(line+"\n")
if not found:
raise Exception("program bug? made it this far without #CHROM in truth VCF?")
else: misses_fd = None
eval_sample_index = eval_vcf.sample_names.index(sample)
truth_sample_index = truth_vcf.sample_names.index(sample)
eval_chr=[]
truth_chr=[]
eval_gen = eval_vcf.lines()
eval_line = eval_gen.next()
eval_chr.append( eval_line.chr )
eval_done = False
n_truth_lines = 0
n_site_hits = 0
n_site_concords = 0
last_truth=(None,None)
last_eval=(None,None)
for truth_line in truth_vcf.lines():
check_sort_order( truth, last_truth, truth_line.chr, truth_line.pos )
truth_genotype=truth_line.get_sample_dict(truth_sample_index)["GT"]
if truth_genotype == "0/0" or truth_genotype=="0|0" or truth_genotype == ".": continue
if debug: print >>sys.stderr,"seeking {}:{}".format( truth_line.chr, truth_line.pos )
n_truth_lines += 1
if n_truth_lines % 1000 == 0: print n_truth_lines
# skip to the correct chromosome
if len(truth_chr) == 0 or truth_chr[-1] != truth_line.chr:
truth_chr.append( truth_line.chr )
# if we've already passed this chr in the eval file, then spin
if not eval_done and truth_line.chr != eval_line.chr and truth_line.chr in eval_chr:
continue
# if we've not already passed this chr, then find it
while not eval_done and eval_line.chr != truth_line.chr:
try:
eval_line = eval_gen.next()
check_sort_order( input, last_eval, eval_line.chr, eval_line.pos )
if debug: print >>sys.stderr,"...next chr={}".format( eval_line.chr )
if eval_chr[-1] != eval_line.chr:
eval_chr.append(eval_line.chr)
print eval_line.chr
except StopIteration: eval_done=True
# try to find the correct position
while not eval_done and eval_line.pos < truth_line.pos \
and eval_line.chr == truth_line.chr:
try:
eval_line = eval_gen.next()
check_sort_order( input, last_eval, eval_line.chr, eval_line.pos )
if debug: print >>sys.stderr,"...next chr:pos={}:{}".format( eval_line.chr, eval_line.pos )
if eval_chr[-1] != eval_line.chr:
eval_chr.append(eval_line.chr)
print eval_line.chr
except StopIteration: eval_done=True
if minqual > 0 and eval_line.qual == '.':
raise Exception("not sure what to do here, we're filtering on qual, but qual is '.'")
if eval_done or eval_line.pos != truth_line.pos \
or eval_line.chr != truth_line.chr \
or ( eval_line.qual != '.' and float(eval_line.qual) < minqual ):
if misses_fd: misses_fd.write(truth_line.line+"\n")
else:
if truth_line.ref != eval_line.ref:
raise Exception("""
Your truth set does not seem to be called on the
same reference as your call set. We're done here.
truth={}
truth_pos={}:{}
truth_ref={}
input={}
input_pos={}:{}
input_ref={}
""".format( truth, truth_line.chr, truth_line.pos,
truth_line.ref, input, eval_line.chr,
eval_line.pos, eval_line.ref ) )
if debug:
print >>sys.stderr,"""
Evaluating:
truth_pos={}:{}
truth_ref={}
truth_alt={}
input_pos={}:{}
input_ref={}
input_alt={}
""".format( truth_line.chr, truth_line.pos,
truth_line.ref, truth_line.alt, eval_line.chr,
eval_line.pos, eval_line.ref, eval_line.alt )
# grab truth NR bases and eval NR bases
eval_genotype=eval_line.get_sample_dict( eval_sample_index)["GT"]
if eval_genotype != ".":
eval_calls_idx = eval_genotype.split("/")
if eval_calls_idx[0] == eval_genotype: eval_calls_idx = eval_genotype.split("|")
if '0' in eval_calls_idx: eval_calls_idx.remove('0')
eval_calls_idx = map(int, eval_calls_idx )
truth_calls_idx = truth_genotype.split("/")
if truth_calls_idx[0] == truth_genotype: truth_calls_idx = truth_genotype.split("|")
if '0' in truth_calls_idx: truth_calls_idx.remove('0')
truth_calls_idx = map(int, truth_calls_idx )
if len(eval_calls_idx) > 0:
n_site_hits += 1
if debug: print >>sys.stderr, "accepting site hit at {}:{}".format(eval_line.chr, eval_line.pos)
elif debug:
print >>sys.stderr, "no NR calls"
for truth_nr in [ truth_line.alt_list[i-1] for i in truth_calls_idx ]:
# if any truth non-reference call is not found on
# the eval line, then we break without counting the
# concordance
if not truth_nr in eval_line.alt_list:
if debug: print >>sys.stderr,"""
non-concordant:
pos={}:{}
truth_ref={}
eval_ref={}
truth_alt={}
eval_alt={}
""".format( truth_line.chr, truth_line.pos,
truth_line.ref, eval_line.ref,
truth_line.alt_list,
eval_line.alt_list )
break
else:
# normal termination of the for loop, so count the
# concordance
if debug: print >>sys.stderr,"""
CONCORDANT:
pos={}:{}
truth_ref={}
eval_ref={}
truth_alt={}
eval_alt={}
""".format( truth_line.chr, truth_line.pos,
truth_line.ref, eval_line.ref,
truth_line.alt_list,
eval_line.alt_list )
n_site_concords += 1
print "n_truth_lines={}, n_site_hits={}, n_site_concords={}, site_hit_frac={}, site_concord_frac={}".format(
n_truth_lines, n_site_hits, n_site_concords,
n_site_hits/float(n_truth_lines),
n_site_concords/float(n_truth_lines)
)
# check that for the eval chromosomes that are also in the truth
# set, that they come in the same order
# first form intersection set
overlap_chr = set(truth_chr).intersection(set(eval_chr))
truth_chr_rev = [ chr for chr in truth_chr if chr in overlap_chr ]
truth_chr_rev.reverse()
for chr in eval_chr:
if chr not in overlap_chr: continue
if chr != truth_chr_rev[-1]:
raise Exception("""
input chromosome ordering doesn't match truth chromosome ordering:
input={}
truth={}
""".format( eval_chr, truth_chr ) )
truth_chr_rev.pop()
if misses_fd: misses_fd.close()
