def make_files_for_graphing(file_prefix, window_sizes, step_size, working_dir,
genome_fai):
in_bed = file_prefix + '.bed'
for ws in window_sizes:
#make bed file with windows and returns genome name and window size variable
genome_and_window = homozygosity_mapping_cybertron.make_windows(
working_dir, genome_fai, ws, step_size).split('.')[0]
print genome_and_window
window_bed = genome_and_window + '.bed'
##bedtools intersect
print(window_bed, in_bed)
with open('temp.bed', "w") as naf_fh:
hom_bt_intersect = subprocess.Popen([
'bedtools', 'intersect', '-a', window_bed, '-b', in_bed, '-c'
],
stdout=naf_fh)
hom_bt_intersect.wait()
##add header
out_bed = file_prefix + '.' + genome_and_window + '.bed'
with open(out_bed, "w") as out_fh, open('temp.bed', "r") as in_fh:
out_fh.write(
delim.join(['chr', 'start', 'end', 'snp_number']) + '\n')
for line in in_fh:
##removing the chr from start of the line
out_fh.write(line[3:])
def make_files_for_graphing(snp_beds, window_size, step_size, genome_fai,
working_dir):
for snp_bed in snp_beds:
for ws in window_size:
#make bed file with windows and returns genome name and window size variable
genome_and_window = homozygosity_mapping_cybertron.make_windows(
working_dir, genome_fai, ws, step_size).split('.')[0]
print(genome_and_window)
window_bed = genome_and_window + '.bed'
##all shared snps
out_file_naf = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.aaf_for_r.txt'
out_file_combined = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.combined_for_r.txt'
##bedtools intersect
with open('temp.bed', "w") as naf_fh:
# hom_bt_intersect = subprocess.Popen(['bedtools', 'intersect', '-a', window_bed, '-b', snp_bed, '-c'], stdout=naf_fh)
# hom_bt_intersect.wait()
hom_bt_intersect = subprocess.Popen([
'bedtools', 'intersect', '-a', window_bed, '-b', snp_bed,
'-wa', '-wb'
],
stdout=naf_fh)
hom_bt_intersect.wait()
with open('temp.bed', "r") as in_fh:
aaf_dict = {}
for line in in_fh:
line = line.rstrip().split(delim)
chr_start_end = delim.join(line[:3])
maaf = float(line[6])
faaf = float(line[7])
if chr_start_end in aaf_dict:
aaf_dict[chr_start_end][0].append(maaf)
aaf_dict[chr_start_end][1].append(faaf)
else:
aaf_dict[chr_start_end] = [[maaf], [faaf]]
##write outfile from dict
with open(out_file_naf,
"w") as outn_fh, open(out_file_combined, "w") as outc_fh:
outn_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
outc_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'value']) +
'\n')
for window in aaf_dict:
ave_maaf = sum(aaf_dict[window][0]) / len(
aaf_dict[window][0])
ave_faaf = sum(aaf_dict[window][1]) / len(
aaf_dict[window][1])
aaf_diff = ave_maaf - ave_faaf
snp_count = len(aaf_dict[window][0])
log_snp_count = math.log(snp_count, 2)
outn_fh.write(window + delim + 'male_aaf' + delim +
str(ave_maaf) + '\n')
outn_fh.write(window + delim + 'female_aaf' + delim +
str(ave_faaf) + '\n')
outc_fh.write(window + delim + 'aaf_male' + delim +
str(ave_maaf) + '\n')
outc_fh.write(window + delim + 'aaf_female' + delim +
str(ave_faaf) + '\n')
outc_fh.write(window + delim + 'aaf_difference' + delim +
str(aaf_diff) + '\n')
# outc_fh.write(window + delim + 'snp_count' + delim + str(snp_count) + '\n')
outc_fh.write(window + delim + 'log2_snp_count' + delim +
str(log_snp_count) + '\n')
'kenny_wgs_0620.chr17_20-40mb.ko_only.xls',
'kenny_wgs_0620.chr17_20-60mb.xls',
'kenny_wgs_0620.chr17_20-60mb.ko_only.xls', 'kenny_wgs_0620.chr17.xls',
'kenny_wgs_0620.chr17.ko_only.xls', 'kenny_wgs_0620.chr17.ko_only.129.xls'
]
beds_to_graph = []
# '''
for file_to_graph in files_to_graph:
bed_to_graph = file_to_graph.rsplit('.', 1)[0] + '.bed'
beds_to_graph.append(bed_to_graph)
make_bed_from_ann_txt(file_to_graph, bed_to_graph)
for bed_to_graph in beds_to_graph:
for ws in window_size:
#make bed file with windows and returns genome name and window size variable
genome_and_window = homozygosity_mapping_cybertron.make_windows(
working_dir, genome_fai, ws, step_size).split('.')[0]
print genome_and_window
window_bed = genome_and_window + '.bed'
##all shared snps
out_bed = bed_to_graph.rsplit('.',
1)[0] + '.' + genome_and_window + '.bed'
##bedtools intersect
with open('temp.bed', "w") as naf_fh:
hom_bt_intersect = subprocess.Popen([
bedtools, 'intersect', '-a', window_bed, '-b', bed_to_graph,
'-c'
],
stdout=naf_fh)
hom_bt_intersect.wait()
##filter for region of interest
if '30mb' in bed_to_graph:
def make_files_for_graphing(snp_beds, window_size, step_size, genome_fai,
working_dir):
for snp_bed in snp_beds:
for ws in window_size:
#make bed file with windows and returns genome name and window size variable
genome_and_window = homozygosity_mapping_cybertron.make_windows(
working_dir, genome_fai, ws, step_size).split('.')[0]
print(genome_and_window)
window_bed = genome_and_window + '.bed'
##all shared snps
out_file_naf1 = snp_bed.rsplit(
'.',
1)[0] + '.' + genome_and_window + '.experiment1.aaf_for_r.txt'
out_file_naf2 = snp_bed.rsplit(
'.',
1)[0] + '.' + genome_and_window + '.experiment2.aaf_for_r.txt'
out_file_combined = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.combined_for_r.txt'
out_file_naf_male = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.male.aaf_for_r.txt'
out_file_naf_female = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.female.aaf_for_r.txt'
out_file_naf_all = snp_bed.rsplit(
'.', 1)[0] + '.' + genome_and_window + '.aaf_for_all.txt'
##bedtools intersect
with open('temp.bed', "w") as naf_fh:
# hom_bt_intersect = subprocess.Popen(['bedtools', 'intersect', '-a', window_bed, '-b', snp_bed, '-c'], stdout=naf_fh)
# hom_bt_intersect.wait()
hom_bt_intersect = subprocess.Popen([
'bedtools', 'intersect', '-a', window_bed, '-b', snp_bed,
'-wa', '-wb'
],
stdout=naf_fh)
hom_bt_intersect.wait()
with open('temp.bed', "r") as in_fh:
aaf_dict = {}
for line in in_fh:
line = line.rstrip().split(delim)
chr_start_end = delim.join(line[:3])
maaf1 = float(line[6])
faaf1 = float(line[7])
maaf2 = float(line[8])
faaf2 = float(line[9])
if chr_start_end in aaf_dict:
aaf_dict[chr_start_end][0].append(maaf1)
aaf_dict[chr_start_end][1].append(faaf1)
aaf_dict[chr_start_end][2].append(maaf2)
aaf_dict[chr_start_end][3].append(faaf2)
else:
aaf_dict[chr_start_end] = [[maaf1], [faaf1], [maaf2],
[faaf2]]
##write outfile from dict
with open(out_file_naf1, "w") as outn1_fh, open(
out_file_naf2, "w") as outn2_fh, open(
out_file_combined, "w") as outc_fh, open(
out_file_naf_male, "w") as outm_fh, open(
out_file_naf_female,
"w") as outf_fh, open(out_file_naf_all,
"w") as outall_fh:
outn1_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
outn2_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
outm_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
outf_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
outc_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'value']) +
'\n')
outall_fh.write(
delim.join(['chr', 'start', 'end', 'test', 'average_aaf'])
+ '\n')
for window in aaf_dict:
ave_maaf1 = sum(aaf_dict[window][0]) / len(
aaf_dict[window][0])
ave_faaf1 = sum(aaf_dict[window][1]) / len(
aaf_dict[window][1])
aaf_diff1 = ave_maaf1 - ave_faaf1
ave_maaf2 = sum(aaf_dict[window][2]) / len(
aaf_dict[window][2])
ave_faaf2 = sum(aaf_dict[window][3]) / len(
aaf_dict[window][3])
aaf_diff2 = ave_maaf2 - ave_faaf2
snp_count = len(aaf_dict[window][0])
log_snp_count = math.log(snp_count, 2)
##first graphing files - by experiment
outn1_fh.write(window + delim + 'male_aaf_1' + delim +
str(ave_maaf1) + '\n')
outn1_fh.write(window + delim + 'female_aaf_1' + delim +
str(ave_faaf1) + '\n')
outn2_fh.write(window + delim + 'male_aaf_2' + delim +
str(ave_maaf2) + '\n')
outn2_fh.write(window + delim + 'female_aaf_2' + delim +
str(ave_faaf2) + '\n')
##first graphing files - by sex
outm_fh.write(window + delim + 'male_aaf_1' + delim +
str(ave_maaf1) + '\n')
outf_fh.write(window + delim + 'female_aaf_1' + delim +
str(ave_faaf1) + '\n')
outm_fh.write(window + delim + 'male_aaf_2' + delim +
str(ave_maaf2) + '\n')
outf_fh.write(window + delim + 'female_aaf_2' + delim +
str(ave_faaf2) + '\n')
##second graphing file
outc_fh.write(window + delim + 'aaf_male_1' + delim +
str(ave_maaf1) + '\n')
outc_fh.write(window + delim + 'aaf_female_1' + delim +
str(ave_faaf1) + '\n')
outc_fh.write(window + delim + 'aaf_difference_1' + delim +
str(aaf_diff1) + '\n')
outc_fh.write(window + delim + 'aaf_male_2' + delim +
str(ave_maaf2) + '\n')
outc_fh.write(window + delim + 'aaf_female_2' + delim +
str(ave_faaf2) + '\n')
outc_fh.write(window + delim + 'aaf_difference_2' + delim +
str(aaf_diff2) + '\n')
# outc_fh.write(window + delim + 'snp_count' + delim + str(snp_count) + '\n')
outc_fh.write(window + delim + 'log2_snp_count' + delim +
str(log_snp_count) + '\n')
##third graphing - combine naf for both experiments
outall_fh.write(window + delim + 'aaf_male_1' + delim +
str(ave_maaf1) + '\n')
outall_fh.write(window + delim + 'aaf_female_1' + delim +
str(ave_faaf1) + '\n')
outall_fh.write(window + delim + 'aaf_male_2' + delim +
str(ave_maaf2) + '\n')
outall_fh.write(window + delim + 'aaf_female_2' + delim +
str(ave_faaf2) + '\n')