def translate2(path):
"Translate the known file with params"
config = build_config(path)
try:
return jsonify(
parsing.translate(config, parsing.tobool(request.args.get('rc')))
)
except Exception as e:
logger.exception('Error While Translating')
return flask.make_response(repr(e), 500)
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)
