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]