def build_config(path):
"Tries to build the config dictionary for the given path"
try:
config = parsing.initial(getabspath(path))
except:
logger.exception(
"Error parsing gbk: %r", getabspath(path, raise_on_missing=False))
raise
parsing.detect_format(config)
for k in VALID_KEYS:
v = request.args.get(k)
if v:
nv = parsing.number(v)
config[k] = v if nv is None else nv
parsing.endBase(config)
parsing.mycoplasma(config)
# fixup nucleotides list
if 'nucleotides' in request.args:
config['nucleotides'] = request.args.getlist('nucleotides')
for key in MAGIC_PARAMS:
if key in request.args:
config[key] = request.args[key]
return config
def translate():
"Translate arbitrary sequence"
try:
# table 4 is for mycoplasma ala:
# http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
table = 1
config = request.get_json()
if parsing.mycoplasma(config):
app.logger.debug('using mycoplasma table=4')
table = 4
seq = Bio.Seq.Seq(config.get('seq'))
rc = parsing.tobool(config.get('complement'))
if rc:
seq = seq.reverse_complement()
trans = Bio.Seq.translate(seq, table)
return jsonify({
'seq': str(seq),
'trans': str(trans)})
except Exception as e:
logger.exception('Error While Translating')
return flask.make_response(repr(e), 500)
