code stringlengths 3 6.57k |
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sns.boxplot(data=df_slice.sort_values(by="segment") |
set_title(f"{period}") |
astimezone() |
tz.gettz('Europe/London') |
local.astimezone(uk) |
print(local.isoformat() |
print(notlocal.isoformat() |
tz.gettz('Asia/Kolkata') |
local.astimezone(ist) |
print(local.isoformat() |
print(notlocal.isoformat() |
tz.gettz('Pacific/Apia') |
local.astimezone(sm) |
print(local.isoformat() |
print(notlocal.isoformat() |
logging.getLogger("") |
namedtuple('CI', ['min', 'max']) |
compute_ci(coverage, var_count) |
sqrt(1/n~ * p~ * (1-p~) |
float(coverage + 4) |
sqrt(p_t * (1-p_t) |
CI._make([min_ci, max_ci]) |
fasta_iter(fasta_name) |
open(fasta_name) |
boolean (x[0]) |
groupby(fh, lambda line: line[0] == ">") |
header.next() |
strip() |
header.next() |
strip() |
split(" ") |
join(s.strip() |
faiter.next() |
cmdline_parser() |
argparse.ArgumentParser(description=__doc__) |
file (vcf format) |
file (for reconstructing cluster sequence) |
file (- for stdout = default) |
vcf_var_to_str(v) |
join(["%s" % x for x in v.ALT]) |
main() |
cmdline_parser() |
parser.parse_args() |
args (not just (len(args) |
LOG.setLevel(logging.INFO) |
LOG.setLevel(logging.DEBUG) |
for (in_file, descr) |
parser.error("%s input file argument missing." % descr) |
sys.exit(1) |
os.path.exists(in_file) |
sys.exit(1) |
for (out_file, descr) |
parser.error("%s output file argument missing." % descr) |
sys.exit(1) |
os.path.exists(out_file) |
sys.exit(1) |
open(args.cluster_file, 'w') |
fasta_iter(args.reffa) |
sys.stderr.write("Only supporting one sequence\n") |
sys.exit(1) |
vcf.VCFReader(filename=args.var_file) |
any([not v.is_snp for v in var_list]) |
sys.stderr.write("WARNING: Only supporting SNPs! Automatically removing others\n") |
LOG.info("Parsed %d SNPs from %s" % (len(var_list) |
all([x.INFO.has_key('AF') |
x.INFO.has_key('DP') |
sorted(var_list, key=lambda x: x.INFO['AF'], reverse=True) |
compute_ci(v.INFO['DP'], int(v.INFO['AF'] * v.INFO['DP']) |
list(zip(var_list, ci_list) |
len(var_ci_list) |
fh_out.write("No variants <-> no clusters!\n") |
fh_out.close() |
sys.exit(0) |
dict() |
append("%s %f" % (var.repr, var.freq) |
append(var) |
range(clu_no+1) |
fh_out.write("# cluster %d (freq. range: %f - %f) |
join([vcf_var_to_str(x) |
sorted(cluster[i,'members'], key = lambda v: v.POS) |
len(v.ALT) |
str(v.ALT[0]) |
fh_out.write(">haplotype-cluster-{}\n{}\n".format(i+1, haplotype) |
fh_out.close() |
print("%d clusters found (written to %s) |
main() |
LOG.info("Successful program exit") |
bin(5) |
pow(2, 2) |
pow(2, 1) |
pow(2, 0) |
pow(2, 4) |
pow(2, 3) |
pow(2, 2) |
pow(2, 1) |
pow(2, 0) |
Solution(object) |
findComplement(self, num) |
bin(num) |
enumerate(reversed(b) |
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