problems.append(msg)
names.append(name)
ns.append(n)
motifs.append(motif)
if valid:
pnames = []
pseqs = []
for name,n,motif in zip(names,ns,motifs):
try:
sites = str2sites(motif)
seq = sites2seq(sites, region=form.cleaned_data['output'], add16k=form.cleaned_data['add16k'])
for i in range(n):
pnames.append(name)
pseqs.append(seq)
except Exception, e:
valid = False
problems.append(e)
if valid:
as_fasta = ''.join(list(entry2str({'name':name,'sequence':seq}, WRAP)
for name,seq in zip(pnames, pseqs)))
c = Context({'results': as_fasta})
else: # not valid
c = Context({'problems':problems})
t = loader.get_template('mttransform/mttransform_seqs.html')
return HttpResponse(t.render(c))
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)
