def run_command():
"""Transform human mtDNA sequence to variable sites."""
# Set up the options parser
usage = "usage: %prog [options] filename"
parser = OptionParser(usage=usage)
parser.add_option('-r',
'--region',
dest='region',
default='hvr1',
help='which predefined sequence region to generate (default hvr1)'
'(one of hvr1, hvr2, hvr1to2, coding, or all)')
parser.add_option('-b',
'--begin',
dest='begin',
type='int',
default=None,
help='define a region to generate (use with --end)')
parser.add_option('-e',
'--end',
dest='end',
type='int',
default=None,
help='define a region to generate (use with --begin)')
# Parse the options
(options, args) = parser.parse_args()
# The filename is always required
if len(args) != 1:
print 'You must provide a filename!'
print "Type 'sites2seq -h' for help."
sys.exit(1)
# make sure the sites file exists
if not os.path.exists(args[0]):
print 'ERROR: Could not find file: %s' % args[0]
sys.exit(1)
count = 0
for entry in csv.reader(open(args[0], 'rU')):
count += 1
if len(entry) != 3:
print 'ERROR: Problem on row %d of the input file' % count
sys.exit(1)
name = entry[0]
n = int(entry[1])
sites = entry[2]
region = options.region
if options.begin is not None and options.end is not None:
if options.end < options.begin:
# wrap through the origin
region = range(options.begin, 16570)+range(1, options.end+1)
else:
region = range(options.begin, options.end+1)
sequence = sites2seq(sites, region=region)
entry = {'name':name, 'sequence':sequence}
for i in range(n):
print entry2str(entry)
2668,
3186,
3189,
3916,
3947,
4089,
4092,
]
count = 0
of = open(ofn, "w")
for entry in open(mtgs_fn, "U"):
count += 1
if count not in expect_to_fail:
entry = entry.strip()
entry = entry.replace("-", "")
try:
sites = seq2sites(entry)
seq = sites2seq(sites, what="all")
seq = seq.replace("-", "")
if entry != seq:
print count, "FAILED"
of.write("%d\n" % count)
else:
print count, "PASSED"
except:
print count, "FAILED"
of.write("%d\n" % count)
of.flush()
of.close()
here = os.path.abspath(os.path.dirname(__file__))
module_dir = os.path.join(here, '..')
genographic_sites_filepath = os.path.join(here, 'genographic_sites.txt')
import sys
sys.path = [module_dir] + sys.path
outfn = os.path.join(here, 'fail_genographic.txt')
outf = open(outfn, 'w')
from oldowan.mitomotifs import sites2seq
from oldowan.mitomotifs import seq2sites
from oldowan.mitomotifs import str2sites
count = 0
for line in open(genographic_sites_filepath, 'rU'):
count += 1
line = line.upper()
sites = str2sites(line)
sites.sort()
seq = sites2seq(sites, region=range(16000,16570))
roundtrip_sites = seq2sites(seq)
roundtrip_sites.sort()
if sites != roundtrip_sites:
outf.write("%d,%s,%s\n" % (count, sites, roundtrip_sites))
else:
print "%d,good" % count
outf.flush()
outf.close()
DLOOPplus = range(15800,16570) + range(1,1500)
dloops_fn = os.path.join(here, 'dloops.fasta')
ofn = os.path.join(here, 'fail_dloop.txt')
fail_fn = os.path.join(here, 'dloop_expect_to_fail.txt')
expect_to_fail = []
for line in open(fail_fn, 'U'):
expect_to_fail.append(int(line.strip()[:-1]))
of = open(ofn, 'w')
count = 0
for entry in fasta(dloops_fn):
count += 1
if count not in expect_to_fail:
try:
sites = seq2sites(entry["sequence"])
seq = sites2seq(sites, region=DLOOPplus)
seq = seq.replace('-', '')
if entry["sequence"] in seq:
print count, entry["name"], sites2str(sites)
else:
print 'FAILED', count, entry["name"]
of.write('%d, %s\n' % (count, entry["name"]))
except Exception, e:
print 'FAILED',e, count, entry["name"]
of.write('%d, %s\n' % (count, entry["name"]))
of.flush()
of.close()