def doGolden(db, ac, DE):
# ########################## db ref
if db in['sp', 'sw', 'swissprot', 'tr', 'trembl']:
db = 'uniprot'
elif db in ['emb', 'dbj']:
db = 'embl'
elif db in ['gb']:
db = 'genbank'
elif db in ['gp']:
db = 'genpept'
elif db in ['ref']:
db = 'refseq'
elif db in ['rdpii']:
db = 'rdpii'
elif db[0:8] == 'embl_wgs':
db = 'embl_wgs'
elif db[0:8] == 'genbank_wgs':
db = 'genbank_wgs'
elif db in ['pir', 'pdb', 'tpg', 'tpe', 'tpd', 'prf']:
return '', '', '', ''
try:
flatFile = Golden.access(db, ac)
except IOError, err:
print >>sys.stderr, err, db, ac
sys.exit()
def doGolden(db, ac, file_format='fasta'):
# ## db ref
if db in ['sp', 'sw', 'swissprot', 'tr', 'trembl']:
db = 'uniprot'
elif db in ['emb', 'dbj']:
db = 'embl'
elif db in ['gb']:
db = 'genbank'
elif db in ['gp']:
db = 'genpept'
elif db in ['ref']:
db = 'refseq'
elif db in ['rdpii']:
db = 'rdpii'
elif db[0:8] == 'embl_wgs':
db = 'embl_wgs'
elif db[0:8] == 'genbank_wgs':
db = 'genbank_wgs'
elif db in ['pir', 'pdb', 'tpg', 'tpe', 'tpd', 'prf']:
return ''
try:
flatFile = Golden.access(db, ac)
except IOError, err:
print >> sys.stderr, err, "%s:%s" % (db, ac)
sys.exit()
def doGoldenMulti(allTaxo,l_input,DE):
idx_res=0
lst_input=l_input.split("\n")
try:
flatFile=Golden.access_new(l_input)
while (flatFile!=None):
db_acc=lst_input[idx_res]
l_db_acc=db_acc.split(":")
acc=l_db_acc[1]
allTaxo[acc]['orgName'], allTaxo[acc]['taxId'], allTaxo[acc]['taxoLight'], allTaxo[acc]['DE'] = parse(flatFile , DE ) #orgName, taxId, taxoLight, description
flatFile=Golden.access_new(l_input)
idx_res+=1
return allTaxo
except IOError, err:
print >>sys.stderr, err, l_input
sys.exit()
def doGolden( db,ac, DE ):
#print "inside doGolden, GOLDENDATA=",GOLDENDATA
########################### db ref
if db in[ 'sp', 'sw','swissprot','tr', 'trembl']:
db = 'uniprot'
elif db in ['emb', 'dbj']:
db = 'embl'
elif db in ['gb']:
db = 'genbank'
elif db in ['gp']:
db = 'genpept'
elif db in ['ref']:
db = 'refseq'
elif db in ['rdpii']:
db = 'rdpii'
elif db in ['pir','pdb','tpg', 'tpe', 'tpd', 'prf']:
return '','','',''
try:
#print "Calling Golden on : ",db,ac
#print "GOLDENDATA=",GOLDENDATA
#print >>f_cards, db+":"+acc
flatFile = Golden.access(db,ac)
except IOError, err:
print >>sys.stderr, err, db, ac
sys.exit()
def doGoldenMulti(allTaxo, l_cards, DE, allTaxId, osVSoc_bdb):
idx_res = 0
lst_input = l_cards.split("\n")
try:
flatFile = Golden.access_new(l_cards)
while (flatFile is not None):
db_acc = lst_input[idx_res]
l_db_acc = db_acc.split(":")
acc = l_db_acc[1]
if acc not in allTaxo:
allTaxo[acc] = {'db': l_db_acc[0]}
allTaxo[acc]['orgName'], allTaxo[acc]['taxId'], allTaxo[acc]['taxoLight'], allTaxo[acc]['DE'] = parse(flatFile, DE) # orgName, taxId, taxoLight, description
allTaxo, allTaxId = extractTaxoFrom_osVSocBDB_multi(acc, allTaxo, allTaxId, osVSoc_bdb)
flatFile = Golden.access_new(l_cards)
idx_res += 1
return allTaxo
except IOError, err:
print >>sys.stderr, err, l_cards
sys.exit()
def doGoldenMulti(allTaxo, l_cards, DE, allTaxId, osVSoc_bdb):
idx_res = 0
lst_input = l_cards.split("\n")
try:
flatFile = Golden.access_new(l_cards)
while (flatFile is not None):
db_acc = lst_input[idx_res]
l_db_acc = db_acc.split(":")
acc = l_db_acc[1]
if acc not in allTaxo:
allTaxo[acc] = {'db': l_db_acc[0]}
allTaxo[acc]['orgName'], allTaxo[acc]['taxId'], allTaxo[
acc]['taxoLight'], allTaxo[acc]['DE'] = parse(
flatFile, DE) # orgName, taxId, taxoLight, description
allTaxo, allTaxId = extractTaxoFrom_osVSocBDB_multi(
acc, allTaxo, allTaxId, osVSoc_bdb)
flatFile = Golden.access_new(l_cards)
idx_res += 1
return allTaxo
except IOError, err:
print >> sys.stderr, err, l_cards
sys.exit()
import Binary
ak = int(input("最小值："))
bk = int(input("最大值："))
L = [1e-2, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-8]
B = []
B_Value = []
G = []
G_Value = []
F = []
F_Value = []
for i in L:
b_value, b = Binary.BinarySearch(ak, bk, i)
g_value, g = Golden.GoldenSearch(ak, bk, i)
f_value, f = Fibonacci.FibonacciSearch(ak, bk, i)
B.append(b)
B_Value.append(b_value)
G.append(g)
G_Value.append(g_value)
F.append(f)
F_Value.append(f_value)
plt.figure(figsize=(12, 8), dpi=80)
plt.figure(1)
ax1 = plt.subplot(321)
plt.plot(L, B, "or") #color='#FF0000'
ax2 = plt.subplot(322)
plt.plot(L, B_Value, "oy")