def efetch(req, id):
logger.info("Asked to fetch Id: %s", id)
session = entrez.EntrezSession(library_root())
abspath = session.fetch_id(id)
path = getrelpath(abspath)
try:
parsing.initial(abspath)
except:
messages.error(req,
"There was a problem loading file '%s', "
"please try again or try a different record."
% path)
return re_search(req)
path = getrelpath(abspath)
remaining_args = dict(req.REQUEST.items())
action = remaining_args.pop('action', 'run')
if action in ['run', 'config']:
return HttpResponseRedirect(
reverse(action, args=[path]) + dict_to_querystring(remaining_args))
else:
logger.error("Unknown action %r", action)
messages.error(req, "Unknown action.")
return re_search(req)
def efetch(id):
logger.info("Asked to fetch Id: %s", id)
searchsession = entrez.EntrezSession(app.config['UPLOADS'])
abspath = searchsession.fetch_id(id)
path = getrelpath(abspath)
try:
parsing.initial(abspath)
except:
flash("There was a problem loading file '%s', "
"please try again or try a different record."
% path)
return re_search()
args = dict(request.args.items())
return redirect(url_for('run_frame', path=path, **args))
def test_translate(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 161
config['endBase'] = 355
result = parsing.translate(config, rc=False)
assert result['seq'] == 'CTGCCTTTTGGTGTCGTTTATTTCGGCTTTTGCCATAGAAGCCAAAGCCCCCAGAAGTTCGCCTTTGTCCCATGTTGGATTGCCGGTCTTACTATCGACCAGACCGGCCAGAATAAGCAGGCCAGCAGACTGGATGAGGTTATGCGTTCTTTCCTTGTCCTTGGCGTCTCTTTCTCTCTTGGCGATTTTCGATGA'
assert result['trans'] == 'LPFGVVYFGFCHRSQSPQKFAFVPCWIAGLTIDQTGQNKQASRLDEVMRSFLVLGVSFSLGDFR*'
def test_trans_myco(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 116
config['endBase'] = 562
config['mycoplasma'] = True
result = parsing.translate(config, rc=True)
assert result['trans'] == 'MASFRIETHIANLRQLEKPSTEQRILILLYDKTDRTPKEERDLKALIRSEKAQEAVKEAKAKASEAKARSSKIAKRERDAKDKERTHNLIQSAGLLILAGLVDSKTGNPTWDKGELLGALASMAKAEINDTKRQEWKEKGDALLAGEKW'
def test_trans_complement(gbkfile):
config = parsing.initial(gbkfile)
config['startBase'] = 116
config['endBase'] = 562
result = parsing.translate(config, rc=True)
assert result['seq'] == 'ATGGCCTCTTTTCGGATTGAAACGCATATCGCTAACCTTCGACAGCTTGAGAAGCCATCGACAGAACAGCGCATCCTGATCTTGCTCTATGACAAGACTGACAGAACGCCAAAAGAGGAAAGAGACCTCAAGGCACTCATCCGGTCGGAAAAAGCGCAGGAAGCCGTAAAAGAGGCTAAAGCCAAAGCATCCGAAGCAAAGGCCAGATCATCGAAAATCGCCAAGAGAGAAAGAGACGCCAAGGACAAGGAAAGAACGCATAACCTCATCCAGTCTGCTGGCCTGCTTATTCTGGCCGGTCTGGTCGATAGTAAGACCGGCAATCCAACATGGGACAAAGGCGAACTTCTGGGGGCTTTGGCTTCTATGGCAAAAGCCGAAATAAACGACACCAAAAGGCAGGAGTGGAAAGAAAAAGGTGATGCGTTATTAGCCGGAGAAAAATGA'
assert result['trans'] == 'MASFRIETHIANLRQLEKPSTEQRILILLYDKTDRTPKEERDLKALIRSEKAQEAVKEAKAKASEAKARSSKIAKRERDAKDKERTHNLIQSAGLLILAGLVDSKTGNPTWDKGELLGALASMAKAEINDTKRQEWKEKGDALLAGEK*'
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 run_cmdline(gbkfile, executorName):
config = parsing.initial(gbkfile)
with getexecutor(executorName) as executor:
config = process('allplots', config, executor=executor)
jid = config.get('allplots_result')
if not Path(jid).exists():
logging.info("Work scheduled, waiting")
output = executor.result(jid, timeout=None)
logging.info("Finished processing %r", gbkfile)
else:
output = jid
logging.info("See output at %r", output)
def test_initial(gbkfile):
result = parsing.initial(gbkfile)
assert 'outputdir' in result
assert result['filename'] == gbkfile
assert 'basename' in result
def rawconfig(rawfile, tmpdir):
return parsing.initial(rawfile, outputdir=str(tmpdir))
def fnaconfig(fnafile, tmpdir):
return parsing.initial(fnafile, outputdir=str(tmpdir))
def gbkconfig(gbkfile, tmpdir):
return parsing.initial(gbkfile, outputdir=str(tmpdir))