def GetExec():
Recs = os.listdir(os.getcwd())
newList = []
j = 0
listdata = dict()
ftime = open('lastChecked.txt', 'r')
prevTime = float(ftime.readline())
ftime.close()
f = open('lastChecked.txt', 'w')
f.write(str(time.time()))
f.close()
k = 0
while k < len(Recs):
(name, ext) = os.path.splitext(Recs[k])
if len(ext) > 2 and not ext == '.pickle':
ListFile = name + ".pickle"
if not os.path.isfile(ListFile) or float(fmt.filemtime(
Recs[k])) > prevTime:
if ext[:3] == ".fa":
if name != "my_seq":
seqIORec = list(SeqIO.parse(Recs[k], 'fasta'))
for i, v in enumerate(seqIORec):
newList.append([v, v.id])
listdata[j] = str(v.id), len(
v.seq), str(name) + str(ext)
rHoward = [
str(v.id),
len(v.seq),
str(name) + str(ext), v
]
mP.spickle(ListFile, rHoward)
j += 1
elif ext[:3] == ".gb":
seqIORec = list(SeqIO.parse(Recs[k], 'genbank'))
for i, v in enumerate(seqIORec):
newList.append([v, v.id])
listdata[j] = str(v.id), len(
v.seq), str(name) + str(ext)
rHoward = [
str(v.id),
len(v.seq),
str(name) + str(ext), v
]
mP.spickle(ListFile, rHoward)
j += 1
else:
if ext[:3] in [".gb", ".fa"]:
rHoward = mP.opickle(ListFile)
listdata[j] = str(rHoward[0]), rHoward[1], rHoward[2]
newList.append([rHoward[3], rHoward[0]])
j += 1
k += 1
return [newList, listdata]
def GetExec():
Recs = os.listdir(os.getcwd())
newList=[]
j = 0
listdata=dict()
ftime = open('lastChecked.txt','r')
prevTime = float(ftime.readline())
ftime.close()
f = open('lastChecked.txt','w')
f.write(str(time.time()))
f.close()
k = 0
while k < len(Recs):
(name, ext) = os.path.splitext(Recs[k])
if len(ext) > 2 and not ext == '.pickle':
ListFile = name + ".pickle"
if not os.path.isfile(ListFile) or float(fmt.filemtime(Recs[k])) > prevTime:
if ext[:3] == ".fa":
if name != "my_seq":
seqIORec = list(SeqIO.parse(Recs[k],'fasta'))
for i,v in enumerate(seqIORec):
newList.append([v,v.id])
listdata[j] = str(v.id),len(v.seq),str(name)+str(ext)
rHoward = [str(v.id),len(v.seq),str(name)+str(ext),v]
mP.spickle(ListFile,rHoward)
j+=1
elif ext[:3] == ".gb":
seqIORec = list(SeqIO.parse(Recs[k],'genbank'))
for i,v in enumerate(seqIORec):
newList.append([v,v.id])
listdata[j] = str(v.id),len(v.seq),str(name)+str(ext)
rHoward = [str(v.id),len(v.seq),str(name)+str(ext),v]
mP.spickle(ListFile,rHoward)
j+=1
else:
if ext[:3] in [".gb",".fa"]:
rHoward = mP.opickle(ListFile)
listdata[j] = str(rHoward[0]),rHoward[1],rHoward[2]
newList.append([rHoward[3],rHoward[0]])
j+=1
k += 1
return [newList,listdata]
def GetExec():
Recs = os.listdir(os.getcwd())
newList = []
j = 0
listdata=dict()
k = 0
p = PDBParser(PERMISSIVE=1)
ftime = open('lastChecked.txt','r')
pT = float(ftime.readline())
ftime.close()
f = open('lastChecked.txt','w')
f.write(str(time.time()))
f.close()
while k < len(Recs):
try:
(name, ext) = os.path.splitext(Recs[k])
if ext=='':
2+2
elif ext==".pdb":
f = name + ".pickle"
newList.append([Recs[k],os.getcwd()])
if not os.path.isfile(f) or float(fmt.filemtime(Recs[k])) > pT:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
pdbRec = p.get_structure(name, Recs[k])
models = pdbRec.get_list()
listdata[j] = str(name), len(models), os.getcwd()+'/'+str(name) + str(ext)
rHoward = [str(name), len(models), str(name) + str(ext)]
mP.spickle(f, rHoward)
else:
rHoward = mP.opickle(f)
listdata[j] = str(rHoward[0]), rHoward[1], rHoward[2]
j += 1
except IOError, e:
print e
k += 1
def GetExec():
Recs = os.listdir(os.getcwd())
newList = []
j = 0
listdata = dict()
k = 0
p = PDBParser(PERMISSIVE=1)
ftime = open('lastChecked.txt', 'r')
pT = float(ftime.readline())
ftime.close()
f = open('lastChecked.txt', 'w')
f.write(str(time.time()))
f.close()
while k < len(Recs):
try:
(name, ext) = os.path.splitext(Recs[k])
if ext == '':
2 + 2
elif ext == ".pdb":
f = name + ".pickle"
newList.append([Recs[k], os.getcwd()])
if not os.path.isfile(f) or float(fmt.filemtime(Recs[k])) > pT:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
pdbRec = p.get_structure(name, Recs[k])
models = pdbRec.get_list()
listdata[j] = str(name), len(
models), os.getcwd() + '/' + str(name) + str(ext)
rHoward = [str(name), len(models), str(name) + str(ext)]
mP.spickle(f, rHoward)
else:
rHoward = mP.opickle(f)
listdata[j] = str(rHoward[0]), rHoward[1], rHoward[2]
j += 1
except IOError, e:
print e
k += 1
def GetExec():
try:
for names in os.listdir(r'.\CurrentCel/'):
os.remove(r'.\CurrentCel/'+names)
os.removedirs(r'.\CurrentCel')
except:
errno
Recs = os.listdir(os.getcwd())
newList=[]
j = 0
PForm = ""
listdata=dict()
GeoUntar = []
k = 0
ftime = open('lastChecked.txt','r')
prevTime = float(ftime.readline())
ftime.close()
f = open('lastChecked.txt','w')
f.write(str(time.time()))
f.close()
for i in Recs:
(nameLeft, ext) = os.path.splitext(i)
if ext == '.tgz':
newList.append([i])
geoListFile = nameLeft + ".pickle"
if not os.path.isfile(geoListFile) or float(fmt.filemtime(i)) > prevTime:
filelib = tarfile.TarFile.gzopen(i)
#Istar = i
GeoUntar.append(filelib)
#print Istar
nameHolder = filelib.getnames()
''''for k,itsgo in enumerate(nameHolder):
try:
if itsgo[-4:] =='.txt' :
if itsgo[0:3] != r"GPL":
newList.append(itsgo)
elif itsgo[0:3] == r"GPL":
PForm = itsgo[:-10]
elif itsgo[-4:] == ".xml":
f = filelib.extractfile(itsgo)
minimal = minidom.parse(f).childNodes[0]
titleText = minimal.childNodes[-2].childNodes[3].childNodes[0].toxml()
except IOError, e:
print e'''
#print nameHolder[:5]
PForm = nameHolder[1][:-10]
#i = nameHolder[0]
#print i
f = filelib.extractfile(nameHolder[0])
minimal = minidom.parse(f).childNodes[0]
titleText = minimal.childNodes[-2].childNodes[3].childNodes[0].toxml()
#print len(minimal.childNodes)
listdata[j] = str(nameLeft[:-4]),titleText, PForm, len(nameHolder)-2
rHoward = [nameLeft,titleText,PForm,len(nameHolder)-2]
mP.spickle(geoListFile,rHoward)
j += 1
else:
rHoward = mP.opickle(geoListFile)
listdata[j] = str(rHoward[0][:-4]),rHoward[1],rHoward[2],rHoward[3]
j += 1
elif ext == r'.tar':
filelib = tarfile.TarFile.taropen(i)
nameHolder = filelib.getnames()
cels = 0
for n in nameHolder:
if n[-7:] == r'.CEL.gz':
cels += 1
"""
sys.path.append(r'..\plugins\Tools\ETOOLSPlugins')
exTool = __import__('ESearch').GetExec('gds',str(nameLeft[:-4]))
esTool = __import__('ESummary').GetExec('gds',str(exTool['IdList'][0]))
titleText = ''
PForm = ''
for line in esTool.split('\n'):
if len(line) > 32:
if line[:34] == '\t<Item Name="title" Type="String">':
titleText = line[34:-8]
elif line[:32] == '\t<Item Name="GPL" Type="String">':
PForm = 'GPL' + str(line[32:-7])
listdata[j] = str(nameLeft[:-4]),titleText, PForm, cels
newList.append([i,PForm])"""
return [newList,listdata]
