def process_seq2sites(handler):
"""Process data submitted in seq2sites form"""
# get posted parameters
content = handler.request.get('content')
wNN = handler.request.get('wNN') == 'yes'
# submission validation and error reporting
problems = []
valid = True
# get the submitted data
content = content.encode('utf8')
# make sure something was submitted
if len(content) == 0:
valid = False
handler.redirect("/seq2sites/")
# determine format
format = None
if content.startswith('>'):
format = 'fasta'
else:
format = 'single_seq'
# pull names and sequence out of submitted content
names = []
seqs = []
if format == 'fasta':
try:
fnames = []
fseqs = []
for entry in fasta(content, 's'):
fnames.append(entry['name'])
fseqs.append(RE_NON_IUPAC.sub('', entry['sequence'].upper()))
names = fnames
seqs = fseqs
except:
valid = False
problems.append('There was an error in the FASTA format')
else:
names = ['']
seqs = [RE_NON_IUPAC.sub('', content.upper())]
# enforce limits for multisequence submissions
if format == 'fasta':
max_length = 0
for seq in seqs:
if len(seq) > max_length:
max_length = len(seq)
if max_length <= LONG_SEQ_CUTOFF:
if len(seqs) > MAX_SEQS_SHORT:
valid = False
problems.append('too many sequences submitted')
elif len(seqs) > MAX_SEQS_LONG:
valid = False
problems.append('too many sequences submitted')
if not valid:
return (False, {'problems': problems})
result_lines = []
sites_by_line = []
for seq in seqs:
try:
sites = seq2sites(seq)
sites_by_line.append(sites)
result_lines.append(sites2str(sites))
except Exception, e:
result_lines.append('There was an error: %s' % e)
for seq in seqs:
try:
sites = seq2sites(seq)
sites_by_line.append(sites)
result_lines.append(sites2str(sites))
except Exception, e:
result_lines.append('There was an error: %s' % e)
if wNN:
names = ['']*len(sites_by_line)
result_lines = []
for sites in sites_by_line:
curr_hvs1 = list(x for x in sites
if int(x.position) in range(16023, 16570)
and not x.is_deletion())
result_lines.append(sites2str(curr_hvs1))
# un-comment the following when it is possible to POST
# a multipart/form-data form from google app engine
#form_fields = {'samples': '\n'.join(hvs1_lines)}
#form_data = urllib.urlencode(form_fields)
#url = "http://nnhgtool.nationalgeographic.com/cgi-bin/classify/classify.ksh"
#result = urlfetch.fetch(url=url,
# payload=form_data,
# method=urlfetch.POST,
# headers={'Content-Type': 'multipart/form-data'})
#logging.info('urlfetch content: %s' % result.content)
results = list(Result(x,y) for x,y in zip(names,result_lines))
template_values = {'results': results}
if wNN:
template_values['show_note'] = 'wNN'