def add_info(opts):
global database
# check arguments
if opts.file is None:
die("Please provide an input file with the -f option")
elif not os.path.exists(opts.file):
die("Cannot find file '%s'" % opts.file)
data = parse_flatfile(opts.file)
for c, d in enumerate(data):
meta = get_metadata(d['Accession No'])
data[c] = dict(d.items() + meta.items())
#print data[c]
database.append(data[c])
# save updated version of DB to pickle
cp.dump(database, open("%s/%s" % (db_loc, database_name), 'wb'))
def add_info(opts):
global database
# check arguments
if opts.file is None:
die("Please provide an input file with the -f option")
elif not os.path.exists(opts.file):
die("Cannot find file '%s'" % opts.file)
data = parse_flatfile(opts.file)
for c, d in enumerate(data):
meta = get_metadata(d["Accession No"])
data[c] = dict(d.items() + meta.items())
# print data[c]
database.append(data[c])
# save updated version of DB to pickle
cp.dump(database, open("%s/%s" % (db_loc, database_name), "wb"))
def test_metadata():
acc = 'AJ511268'
exp = {
'Molecule Type': 'genomic DNA',
'Topology': 'linear',
'Organism': 'Pseudomonas aeruginosa',
'Taxonomy': 'Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas',
'Taxon ID': '287',
'Strain': '',
'Description': 'Pseudomonas aeruginosa partial type 1 integron In182',
'Keywords': 'aac(3)-Ic gene; aminoglycoside acetyltransferase; blaVIM-2 gene; cmlA7 gene; CMLA7 protein; DNA integrase; integron; intI1 gene; qacEdelta1 gene; QacEdelta1 multidrug exporter; VIM-2 metallo-beta-lactamase',
'Reference Location': 'Antimicrob. Agents Chemother. 47(5):1746-1748(2003).',
'PubMed ID': '12709352',
'Notes': '',
'URL': 'http://www.ebi.ac.uk/ena/data/view/AJ511268',
'Sequence': '',
'First Release': '2003-04-24',
'Last Updated': '2005-04-15'
}
got = ena_metadata.get_metadata(acc)
assert got == exp
def initiate_test_sequence(opt):
data = get_metadata(opt.query)
print data
def initiate_test_sequence(opt):
data = get_metadata(opt.query)
print data