Python ScreedDB.keys方法代码示例

# 需要导入模块: from screed import ScreedDB [as 别名]
# 或者: from screed.ScreedDB import keys [as 别名]
class _ScreedSeqInfoDict_ByName(object, UserDict.DictMixin):

    """seqInfoDict implementation that uses names to retrieve records."""

    def __init__(self, filepath):
        self.sdb = ScreedDB(filepath)

    def __getitem__(self, k):
        v = self.sdb[k]
        return _ScreedSequenceInfo(k, v)

    def keys(self):
        return self.sdb.keys()

    def itervalues(self):
        i = 0
        max_index = len(self.sdb)
        while i < max_index:
            v = self.sdb.loadRecordByIndex(i)
            yield _ScreedSequenceInfo(v.name, v)
            i += 1

    def iteritems(self):
        for v in self.itervalues():
            yield v.record.name, v

# 需要导入模块: from screed import ScreedDB [as 别名]
# 或者: from screed.ScreedDB import keys [as 别名]
class Test_xeno_fasta:
    """
    Test screed methods on the xeno fasta file
    """
    def setup(self):
        self.db = ScreedDB(xeno + '_screed')

    def tearDown(self):
        del self.db
        gc.collect()

    def test_iteration(self):
        """
        Runs through the database, accessing each element by index and then by
        name
        """
        for idx in xrange(0, len(self.db)):
            rcrd = self.db.loadRecordByIndex(idx)
            nameRcrd = self.db[rcrd.name]
            assert rcrd == nameRcrd

    def test_dict_stuff(self):
        """
        Tests some dictionary methods on the database
        """
        keys = self.db.keys()
        ikeys = list(self.db.iterkeys())
        assert sorted(keys) == sorted(ikeys)
        del keys
        del ikeys
        gc.collect()

    def test_contains(self):
        for k in self.db:
            assert k in self.db

        assert not 'FOO' in self.db

    def test_get(self):
        for k in self.db:
            record = self.db.get(k)
            assert record.name == k

            record = self.db[k]
            assert record.name == k

        assert self.db.get('FOO') == None
        try:
            self.db['FOO']
            assert False, "the previous line should raise a KeyError"
        except KeyError:
            pass

    def test_missing(self):
        """
        Make sure that unsupported dict attributes are actually missing.
        """
        db = self.db

        try:
            db.clear()
            assert 0
        except AttributeError:
            pass

        try:
            db.update({})
            assert 0
        except AttributeError:
            pass

        try:
            db.clear()
            assert 0
        except AttributeError:
            pass

        try:
            db.setdefault(None)
            assert 0
        except AttributeError:
            pass

        try:
            db.pop()
            assert 0
        except AttributeError:
            pass

        try:
            db.popitem()
            assert 0
        except AttributeError:
            pass

    def test_certain_records(self):
        """
        Pulls first, last, middle and few other records out of database and
        compares them to known quantities
        """
#.........这里部分代码省略.........

# 需要导入模块: from screed import ScreedDB [as 别名]
# 或者: from screed.ScreedDB import keys [as 别名]
class myFirstUI(Directory):
	_q_exports = ['','firstkMer','kmerNeighborhood']
	theK=17
	
	def __init__(self):
		# the 12 is the size of K which can be set here:
		#self.ktable=khmer.new_ktable(12)
		self.ktable=khmer.new_hashbits(self.theK,1e9,4)
		#specify the files you want to load, they have to be screed files
		names=('chr01.fsa','chr02.fsa','chr03.fsa','chr04.fsa','chr05.fsa','chr06.fsa','chr07.fsa',
		'chr08.fsa','chr09.fsa','chr10.fsa','chr11.fsa','chr12.fsa','chr13.fsa','chr14.fsa','chr15.fsa','chr16.fsa')

		for name in names:
			self.fadb=ScreedDB(name)
			print name
			keys=self.fadb.keys()
			for key in keys:
				s=self.fadb[key]['sequence']
				self.ktable.consume(str(s))
		print "done consuming"
		
	def _q_index(self):
		return "kmer browser database"

	def firstkMer(self):
		i=0
		while self.ktable.get(i)==0:
			i+=1
		return self.ktable.reverse_hash(i)

	def addAllKmers(self,currentKmer,depth,maxDepth):
		if depth<maxDepth:
			L=['A','C','G','T']
			rawStringLead=currentKmer[0:(self.theK-1)]
			rawStringTrail=currentKmer[1:self.theK]
			for l in L:
				s=rawStringTrail+l
				if self.ktable.get(s)!=0: 
					self.lines[currentKmer+'	'+s]=1
					if not s in self.liste:
						self.liste[s]=depth+1
						self.addAllKmers(s,depth+1,maxDepth)
				s=l+rawStringLead
				if self.ktable.get(s)!=0:
					self.lines[currentKmer+'	'+s]=1
					if not s in self.liste:
						self.liste[s]=depth+1
						self.addAllKmers(s,depth+1,maxDepth)
			
	def kmerNeighborhood(self):
		request=quixote.get_request()
		form=request.form
		n=int(form['n'])
		print n
		self.liste=dict()
		self.lines=dict()
		self.liste.clear()
		self.lines.clear()
		self.liste[str(form['kmer'])]=0
		self.addAllKmers(str(form['kmer']),0,n)
		S=str(len(self.liste))+'\n'
		for l in self.liste.keys():
			S=S+l+'	'+str(self.liste[l])+'\n'
		for l in self.lines.keys():
			S=S+l+'\n'
		return S
	
	def interface(self):
		myVariable=templatesdir
		template = env.get_template('kMerBrowserInterface.html')
		return template.render(locals())

# 需要导入模块: from screed import ScreedDB [as 别名]
# 或者: from screed.ScreedDB import keys [as 别名]
#typing: $ records
#   PRODUCES: [{'description': 'Drosophila melanogaster birnavirus SW-2009a strain DBV segment A, complete sequence', 'id': 0, 'name': 'gi|262225302|gb|GQ342962.1|', 'sequence': <_screed_attr 'sequence'>}, {'description': 'Drosophila melanogaster birnavirus SW-2009a strain DBV segment B, complete sequence', 'id': 1, 'name': 'gi|262225305|gb|GQ342963.1|', 'sequence': <_screed_attr 'sequence'>}]
#len(record['sequence'])
#   3014
#record['sequence']
#   <_screed_attr 'sequence'>
print "\n\n\n"
#print "Printing a count: all birna records (should equal to 2)...\n"
#print len(birnarecords)
print "\n\n\n"
#print "\nPrinting sequence of last record.\n\t"

#print record['sequence']

print "\nPrinting first record\n\t"
segmentA = birna_x_virusdb[birna_x_virusdb.keys()[0]]
#print segmentA

#segment
#   {'description': 'Drosophila melanogaster birnavirus SW-2009a strain DBV segment A, complete sequence', 'id': 0, 'name': 'gi|262225302|gb|GQ342962.1|', 'sequence': <_screed_attr 'sequence'>}

print "\nPrinting second record...\n\t"
segmentB = birna_x_virusdb[birna_x_virusdb.keys()[1]]
#print segmentB

print "\nPrinting third record\n\t"
segmentXA = birna_x_virusdb[birna_x_virusdb.keys()[2]]
#print segmentXA

print "\nPrinting fourth record...\n\t"
segmentXB = birna_x_virusdb[birna_x_virusdb.keys()[3]]