def main():
"""
The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
snp_files = args
if len(snp_files)<2:
parser.error("Need more than two SNP files.")
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
for (required_opt, opt_descr) in [
(opts.seq_len, "sequence length"),
]:
if not required_opt:
LOG.fatal("Missing %s argument" % opt_descr)
sys.exit(1)
LOG.info("Init sig-level=%f" % (SIG_LEVEL))
excl_pos = []
if opts.fexclude:
excl_pos = read_exclude_pos_file(opts.fexclude)
LOG.info("Excluding %d positions" % len(excl_pos))
snps = []
for snp_file in snp_files:
more_snps = snp.parse_snp_file(snp_file)
snps.extend(more_snps)
LOG.info("Parsed %d SNPs from %s" % (len(more_snps), snp_file))
print "#coldspots"
print "#excluding positions listed in %s" % opts.fexclude
print "#considering snvs listed in %s" % (', '.join(snp_files))
find_coldspot_regions(snps, opts.seq_len, excl_pos)
def main():
"""
The main function
"""
parser = cmdline_parser()
(opts, args) = parser.parse_args()
if len(args):
parser.error("Unrecognized arguments found: %s." % (
' '.join(args)))
sys.exit(1)
if opts.verbose:
LOG.setLevel(logging.INFO)
if opts.debug:
LOG.setLevel(logging.DEBUG)
for (required_opt, opt_descr) in [(opts.win_size, "window size"),
(opts.step_size, "step size"),
(opts.snp_file, "SNP file"),
(opts.seq_len, "sequence length")]:
if not required_opt:
LOG.fatal("Missing %s argument" % opt_descr)
sys.exit(1)
excl_pos = []
if opts.fexclude:
excl_pos = read_exclude_pos_file(opts.fexclude)
LOG.info("Excluding %d positions" % len(excl_pos))
snps = snp.parse_snp_file(opts.snp_file)
LOG.info("Parsed %d SNPs from %s" % (len(snps), opts.snp_file))
find_hotspot_windows(snps, opts.seq_len, opts.win_size,
opts.step_size, excl_pos)
def main():
"""The main function
"""
parser = cmdline_parser()
args = parser.parse_args()
# FIXME catch unrecognized args (not just (len(args)
if args.verbose:
LOG.setLevel(logging.INFO)
if args.debug:
LOG.setLevel(logging.DEBUG)
for (in_file, descr) in [(args.var_file, "variant file")]:
if not in_file:
parser.error("%s input file argument missing." % descr)
sys.exit(1)
if not os.path.exists(in_file) and in_file != "-":
sys.stderr.write(
"file '%s' does not exist.\n" % in_file)
sys.exit(1)
for (out_file, descr) in [(args.cluster_file, "cluster output file")]:
if not out_file:
parser.error("%s output file argument missing." % descr)
sys.exit(1)
if os.path.exists(out_file) and out_file!="-":
sys.stderr.write(
"Cowardly refusing to overwrite existing"
" output file '%s'.\n" % out_file)
sys.exit(1)
# A lot of code for supporting legacy SNP format.
#
# FIXME this and MetaVar() should use vcf by default and just
# convert snp to vcf
#
is_vcf = False
if HAVE_VCF_MODULE:
if args.var_file == '-':
vcf_fh = sys.stdin
else:
vcf_fh = open(args.var_file)
# FIXME gzip support
vcf_reader = vcf.VCFReader(vcf_fh)
try:
var_list = [MetaVar(vcf_var=r)
for r in vcf_reader]
is_vcf = True
except:
raise
if vcf_fh != sys.stdin:
vcf_fh.close()
is_snp = False
if not is_vcf and HAVE_SNP_MODULE:
try:
var_list = [MetaVar(snp_var=s)
for s in snp.parse_snp_file(args.var_file)]
is_snp = True
except IndexError:
pass
if not is_snp and not is_vcf:
LOG.error("Can't parse %s. Tried the following formats: %s" % (
args.var_file, ', '.join(SUPPORTED_FORMATS)))
sys.exit(1)
LOG.info("Parsed %d SNPs from %s" % (len(var_list), args.var_file))
var_list = sorted(var_list, key=lambda x: x.freq, reverse=True)
if args.cluster_file == '-':
fh_out = sys.stdout
else:
fh_out = open(args.cluster_file, 'w')
if len(var_list)==0:
fh_out.write("No SNPs <-> no clusters!\n")
if fh_out != sys.stdout:
print "No SNPs <-> no clusters!"
fh_out.close()
sys.exit(0)
cluster = dict()
clu_no = 0
seed = var_list[0]
#cluster[clu_no,'members'] = ["%s %f" % (seed.repr, seed.freq)]
cluster[clu_no,'members'] = ["%s" % (seed.repr)]
cluster[clu_no,'min'] = seed.min_ci
cluster[clu_no,'max'] = seed.max_ci
for var in var_list[1:]:
LOG.debug("checking %s %f: max_ci %f vvar. clu_min %f" % (
var.repr, var.freq, var.max_ci, cluster[clu_no,'min']))
if var.max_ci > cluster[clu_no,'min']:
#cluster[clu_no,'members'].append("%s %f" % (var.repr, var.freq))
cluster[clu_no,'members'].append("%s" % (var.repr))
else:
clu_no += 1
seed = var
#cluster[clu_no,'members'] = ["%s %f" % (seed.repr, seed.freq)]
cluster[clu_no,'members'] = ["%s" % (seed.repr)]
cluster[clu_no,'min'] = seed.min_ci
cluster[clu_no,'max'] = seed.max_ci
for i in range(clu_no+1):
fh_out.write("cluster %d (freq. range: %f - %f): %s\n" % (
i+1, cluster[i,'min'], cluster[i,'max'],
', '.join(cluster[i,'members'])))
if fh_out != sys.stdout:
fh_out.close()
print "%d clusters found (written to %s)" % (clu_no+1, fh_out.name)
def main():
"""The main function
"""
parser = cmdline_parser()
args = parser.parse_args()
# FIXME catch unrecognized args (not just (len(args)
if args.verbose:
LOG.setLevel(logging.INFO)
if args.debug:
LOG.setLevel(logging.DEBUG)
for (in_file, descr) in [(args.var_file, "variant file")]:
if not in_file:
parser.error("%s input file argument missing." % descr)
sys.exit(1)
if not os.path.exists(in_file) and in_file != "-":
sys.stderr.write("file '%s' does not exist.\n" % in_file)
sys.exit(1)
for (out_file, descr) in [(args.cluster_file, "cluster output file")]:
if not out_file:
parser.error("%s output file argument missing." % descr)
sys.exit(1)
if os.path.exists(out_file) and out_file != "-":
sys.stderr.write("Cowardly refusing to overwrite existing"
" output file '%s'.\n" % out_file)
sys.exit(1)
# A lot of code for supporting legacy SNP format.
#
# FIXME this and MetaVar() should use vcf by default and just
# convert snp to vcf
#
is_vcf = False
if HAVE_VCF_MODULE:
if args.var_file == '-':
vcf_fh = sys.stdin
else:
vcf_fh = open(args.var_file)
# FIXME gzip support
vcf_reader = vcf.VCFReader(vcf_fh)
try:
var_list = [MetaVar(vcf_var=r) for r in vcf_reader]
is_vcf = True
except:
raise
if vcf_fh != sys.stdin:
vcf_fh.close()
is_snp = False
if not is_vcf and HAVE_SNP_MODULE:
try:
var_list = [
MetaVar(snp_var=s) for s in snp.parse_snp_file(args.var_file)
]
is_snp = True
except IndexError:
pass
if not is_snp and not is_vcf:
LOG.error("Can't parse %s. Tried the following formats: %s" %
(args.var_file, ', '.join(SUPPORTED_FORMATS)))
sys.exit(1)
LOG.info("Parsed %d SNPs from %s" % (len(var_list), args.var_file))
var_list = sorted(var_list, key=lambda x: x.freq, reverse=True)
if args.cluster_file == '-':
fh_out = sys.stdout
else:
fh_out = open(args.cluster_file, 'w')
if len(var_list) == 0:
fh_out.write("No SNPs <-> no clusters!\n")
if fh_out != sys.stdout:
print "No SNPs <-> no clusters!"
fh_out.close()
sys.exit(0)
cluster = dict()
clu_no = 0
seed = var_list[0]
#cluster[clu_no,'members'] = ["%s %f" % (seed.repr, seed.freq)]
cluster[clu_no, 'members'] = ["%s" % (seed.repr)]
cluster[clu_no, 'min'] = seed.min_ci
cluster[clu_no, 'max'] = seed.max_ci
for var in var_list[1:]:
LOG.debug("checking %s %f: max_ci %f vvar. clu_min %f" %
(var.repr, var.freq, var.max_ci, cluster[clu_no, 'min']))
if var.max_ci > cluster[clu_no, 'min']:
#cluster[clu_no,'members'].append("%s %f" % (var.repr, var.freq))
cluster[clu_no, 'members'].append("%s" % (var.repr))
else:
clu_no += 1
seed = var
#cluster[clu_no,'members'] = ["%s %f" % (seed.repr, seed.freq)]
cluster[clu_no, 'members'] = ["%s" % (seed.repr)]
cluster[clu_no, 'min'] = seed.min_ci
cluster[clu_no, 'max'] = seed.max_ci
for i in range(clu_no + 1):
fh_out.write("cluster %d (freq. range: %f - %f): %s\n" %
(i + 1, cluster[i, 'min'], cluster[i, 'max'], ', '.join(
cluster[i, 'members'])))
if fh_out != sys.stdout:
fh_out.close()
print "%d clusters found (written to %s)" % (clu_no + 1, fh_out.name)
