def getPairTag(fin, f1pairWithTag_info, sep='\t'):
'''
:param fin: fin pair
:param f1pairWithTag_info: fout
:return:
tag
0, TMP_SP
1, TMP_TMP
2, SP_SP
'''
do = DataOperation('uniprot', 'uniprot_sprot')
with open(f1pairWithTag_info, 'w') as fo:
for pa, pb in getPairs(fin, sep=sep, title=False):
print('%s\t%s' % (pa, pb))
result = tagPair(pa, pb, do)
if result == None: continue
proA = ensomblePortein(result[0])
proB = ensomblePortein(result[1])
for v in proA.values():
fo.write(str(v))
fo.write('\t')
for v in proB.values():
fo.write(str(v))
fo.write('\t')
fo.write(str(result[2]))
fo.write('\n')
fo.flush()
def getPairInfo_TMP_nonTMP(fin, fout, sep='\t', checkTMP=True, keepOne=False):
'''
:param fin:
Q7BCK4 B6JN06
E7QG89 B2FN41
:param fout:
TMP + nonTMP ['accession', 'name', 'length', 'noX', 'inlenRange', 'subcellularLocations', 'seq']
Q7BCK4 ICSA_SHIFL 1102 True True ['Periplasm', 'Secreted', 'Cell surface', 'Cell outer membrane'] MNQIHKFFCNMTQCSQGGAGELPTVKEKTCKLSFSPFVVGASLLLGGPIAFATPLSGTQELHFSEDNYEKLLTPVDGLSPLGAGEDGMDAWYITSSNPSHASRTKLRINSDIMISAGHGGAGDNNDGNSCGGNGGDSITGSDLSIINQGMILGGSGGSGADHNGDGGEAVTGDNLFIINGEIISGGHGGDSYSDSDGGNGGDAVTGVNLPIINKGTISGGNGGNNYGEGDGGNGGDAITGSSLSVINKGTFAGGNGGAAYGYGYDGYGGNAITGDNLSVINNGAILGGNGGHWGDAINGSNMTIANSGYIISGKEDDGTQNVAGNAIHITGGNNSLILHEGSVITGDVQVNNSSILKIINNDYTGTTPTIEGDLCAGDCTTVSLSGNKFTVSGDVSFGENSSLNLAGISSLEASGNMSFGNNVKVEAIINNWAQKDYKLLSADKGITGFSVSNISIINPLLTTGAIDYTKSYISDQNKLIYGLSWNDTDGDSHGEFNLKENAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEKNTYSGFTNINAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNINAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSLGAVLGNDNSKTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSSDKNAFIQKGRIVAGSYDYRLKQGTVSGLNTNKWYLTSQMDNQESKQMSNQESTQMSSRRASSQLVSSLNLGEGSIHTWRPEAGSYIANLIAMNTMFSPSLYDRHGSTIVDPTTGQLSETTMWIRTVGGHNEHNLADRQLKTTANRMVYQIGGDILKTNFTDHDGLHVGIMGAYGYQDSKTHNKYTSYSSRGTVSGYTAGLYSSWFQDEKERTGLYMDAWLQYSWFNNTVKGDGLTGEKYSSKGITGALEAGYIYPTIRWTAHNNIDNALYLNPQVQITRHGVKANDYIEHNGTMVTSSGGNNIQAKLGLRTSLISQSCIDKETLRKFEPFLEVNWKWSSKQYGVIMNGMSNHQIGNRNVIELKTGVGGRLADNLSIWGNVSQQLGNNSYRDTQGILGVKYTF B6JN06 G6PI_HELP2 545 True True ['Cytoplasm'] MLTQLKTYPKLLKHYEEIKEAHMRDWFSKDKERASRYFVQLESLSLDYSKNRLNDTTLKLLFELANDCSLKEKIEAMFKGEKINTTEKRAVLHTALRSLNDTEILLDNMEVLKSVRSVLKRMRAFSDSVRSGKRLGYTNQVITDIVNIGIGGSDLGALMVCTALKRYGHPRLKMHFVSNVDGTQILDVLEKINPASTLFIVASKTFSTQETLTNALTARKWFVERSGDEKHIAKHFVAVSTNKEAVQQFGIDEHNMFEFWDFVGGRYSLWSAIGLSIMIYLGKKNFNALLKGAYLMDEHFRNAPFESNLPVLMGLIGVWYINFFQSKSHLIAPYDQYLRHFPKFIQQLDMESNGKRISKKGETIPYDTCPVVWGDMGINAQHAFFQLLHQGTHLIPIDFIASLDKKPNAKGHHEILFSNVLAQAQAFMKGKSYEEALGELLFKGLDKDEAKDLAHHRVFFGNRPSNILLLEKISPSNIGALVALYEHKVFVQGVIWDINSFDQWGVELGKELAVPILQELEGHKSNAYFDSSTKHLIELYKNYNQ
E7QG89 SEC11_YEASZ 167 True True ['Endoplasmic reticulum membrane'] MNLRFELQKLLNVCFLFASAYMFWQGLAIATNSASPIVVVLSGSMEPAFQRGDILFLWNRNTFNQVGDVVVYEVEGKQIPIVHRVLRQHNNHADKQFLLTKGDNNAGNDISLYANKKIYLNKSKEIVGTVKGYFPQLGYITIWISENKYAKFALLGMLGLSALLGGE B2FN41 EX7L_STRMK 443 True True ['Cytoplasm'] MQPRNNDILTPSQLNTLARDLLEGSFPAIWVEAELGSVARPASGHLYFTLKDARAQLRAAMFRMKAQYLKFVPREGMRVLVRGKVTLYDARGEYQMVLDHMEEAGEGALRRAFEELKARLEAEGLFDPARKRPLPTHVQRLAVITSPTGAAVRDVLSVLGRRFPLLEVDLLPTLVQGSSAAAQITRLLQAADASGRYDVILLTRGGGSLEDLWAFNDEALARAIAASRTPVVSAVGHETDFSLSDFAADLRAPTPSVAAELLVPDQRELALRLRRTAARMVQLQRHAMQQAMQRADRALLRLNAQSPQARLDLLRRRQLDLGRRLHAVFNQQQERRAARLRHAAAVLRGHHPQRQLDAMQRRLAALRGRPQAAMQRLLERDALRLRGLARSLEAVSPLATVARGYSILTRTDDGTLVRKVNQVQPGDALQARVGDGVIDVQVK
:return:
fin = 'file/_1pair.txt'
fout = 'file/_2pair_info.txt'
getPairInfo_TMP_nonTMP(fin,fout)
'''
do = DataOperation('uniprot', 'uniprot_sprot')
with open(fout, 'w') as fo:
for pa, pb in getPairs(fin, sep=sep, title=False):
print('%s\t%s' % (pa, pb))
result = getTaN(pa, pb, do, checkTMP=checkTMP, keepOne=keepOne)
if result == None: continue
tmp = ensomblePortein(result[0])
nontmp = ensomblePortein(result[1])
for v in tmp.values():
fo.write(str(v))
fo.write('\t')
for v in nontmp.values():
fo.write(str(v))
fo.write('\t')
fo.write('\n')
fo.flush()
def loadTest(self,fin_pair,dir_in,onehot=False,is_shuffle=False,limit=0):
"""
:param fin_pair:
:param dir_in:
:param limit:
:param onehot:
:return: data,label
"""
x_test = []
y_test = []
count = 0
for proteins in getPairs(fin_pair, title=False):
count = count +1
xelem,yelem = self.loadPpair(dir_in, proteins)
x_test.append(xelem)
y_test.append(yelem)
# eachfile = os.path.join(dir_in, '%s_%s.npy' % (proteins[0], proteins[1]))
# # print(count,eachfile)
# try:
# # elem = np.load(os.path.join(dir_in, eachfile))
# elem = np.load(eachfile)
# x_test.append(elem)
# # loading test dataset or positive dataset
# if len(proteins) < 3 or proteins[2] == '1':
# y_test.append(1)
# else:
# y_test.append(0)
# except:
# print('not find feature of this pair', str(proteins))
if count == limit:break
data = np.array(x_test)
label = np.array(y_test)
return self.subprocess(data,label,test_size=0, random_state=123,onehot=onehot,is_shuffle=is_shuffle)
def loadTest(self, fin_pair, dir_in, onehot=False, is_shuffle=False):
"""
:param fin_pair:
:param dir_in:
:param limit:
:param onehot:
:return: data,label
"""
x_test = []
y_test = []
for proteins in getPairs(fin_pair, title=False):
eachfile = os.path.join(dir_in,
'%s_%s.npy' % (proteins[0], proteins[1]))
try:
elem = np.load(os.path.join(dir_in, eachfile))
x_test.append(elem)
# loading test dataset or positive dataset
if len(proteins) < 3 or proteins[2] == '1':
y_test.append(1)
else:
y_test.append(0)
except:
print('not find feature of this pair', str(proteins))
data = np.array(x_test)
label = np.array(y_test)
return self.subprocess(data,
label,
test_size=0,
random_state=123,
onehot=onehot,
is_shuffle=is_shuffle)
def loadPair(self, fin_pair, dir_in, limit=0):
positive = []
negative = []
row = 0
for proteins in getPairs(fin_pair, title=False):
eachfile = os.path.join(dir_in,
'%s_%s.npy' % (proteins[0], proteins[1]))
try:
elem = np.load(os.path.join(dir_in, eachfile))
# loading test dataset or positive dataset
if len(proteins) < 3 or proteins[2] == '1':
positive.append(elem)
row = row + 1
else:
negative.append(elem)
except:
print('not find feature of this pair', str(proteins))
if limit != 0 and limit < min(len(positive), len(negative)):
positive, negative = positive[:limit], negative[:limit]
print('positive : ', len(positive))
print('negative : ', len(negative))
positive = np.stack(positive)
negative = np.stack(negative) if negative != [] else []
self.positive = positive
self.negative = negative
def getPairseq(self,
fin_fasta,
fin_ID_pair,
fout_seq_pair,
saveID=False,
num=0,
multi=True):
# fd = FastaDealer()
# fin_fasta = '/home/jjhnenu/data/PPI/release/featuredb/positiveV1.fasta'
# fin_ID_pair = '/home/jjhnenu/data/PPI/release/pairdata/positive_2049.txt'
# fout_seq_pair = '/home/jjhnenu/data/PPI/release/pairdata/positive_2049_seq.txt'
# mydict = fd.getDict(fin_fasta, multi=True)
mydict = self.getDict(fin_fasta, multi=multi)
file_num = 0
count = 0
fout_seq_pair = fout_seq_pair
myfout_seq_pair = fout_seq_pair.split('.')[0] + '_%d.txt' % file_num
myfout_seq_ID_pair = fout_seq_pair.split(
'.')[0] + '_ID_%d.txt' % file_num
fo = open(myfout_seq_pair, 'w')
fo_ID = open(myfout_seq_ID_pair, 'w')
for record in getPairs(fin_ID_pair, sep='\t', title=False):
a = record[0]
b = record[1]
c = ''
if len(record) == 3:
c = record[2]
if saveID:
# fo.write('>%s %s\n' % (a, c))
fo.write('>%s\n' % a)
fo.flush()
fo.write(mydict[a] + '\n')
fo.flush()
if saveID:
# fo.write('>%s %s\n' % (b, c))
fo.write('>%s\n' % b)
fo_ID.write('%s\t%s\t%s\n' % (a, b, c))
fo.write(mydict[b] + '\n')
fo.flush()
count = count + 1
if num != 0 and count == num:
file_num = file_num + 1
count = 0
fo.close()
fo_ID.close()
myfout_seq_pair = fout_seq_pair.split(
'.')[0] + '_%d.txt' % file_num
myfout_seq_ID_pair = fout_seq_pair.split(
'.')[0] + '_ID_%d.txt' % file_num
fo = open(myfout_seq_pair, 'w')
fo_ID = open(myfout_seq_ID_pair, 'w')
fo.close()
fo_ID.close()
print()
def base_compose(self,
dirout_feature,
fin_pair,
dir_feature_db,
feature_type='V_PSSM',
fout_pair=''):
check_path(dirout_feature)
fo = open(fout_pair, 'w') if fout_pair != '' else None
row = 0
for pairs in getPairs(fin_pair):
a = pairs[0]
b = pairs[1]
# print(pairs) # ['O35668', 'P00516']
fa = os.path.join(dir_feature_db, a + '.npy')
fb = os.path.join(dir_feature_db, b + '.npy')
row = row + 1
print('loading %d th feature pair' % row)
if not (os.access(fa, os.F_OK) and os.access(fb, os.F_OK)):
print(
'===============features of pairs not found %s %s================'
% (a, b), os.access(fa, os.F_OK), os.access(fb, os.F_OK))
continue
pa = np.load(fa, allow_pickle=True)
pb = np.load(fb, allow_pickle=True)
if (len(pa) < 50 or len(pa) > 2000
or max(pa) > 20) or (len(pb) < 50 or len(pb) > 2000
or max(pb) > 20):
print('wrong length or x')
continue
if fo != None:
fo.write('%s\t%s\n' % (a, b))
fo.flush()
# padding
if feature_type == Feature_type.V_PSSM:
pc = self.padding_PSSM(pa, pb, vstack=True)
elif feature_type == Feature_type.H_PSSM:
pc = self.padding_PSSM(pa, pb, vstack=False)
elif feature_type == Feature_type.SEQ_1D:
pc = self.padding_seq1D(pa, pb, vstack=False)
# elif feature_type == Feature_type.SEQ_1D_OH:pc = self.padding_seq1D(pa,pb,vstack=False)
elif feature_type == Feature_type.SEQ_2D:
pc = self.padding_seq2D(pa, pb)
else:
print('incoreect feature_type')
return
# 保存padding后的成对特征
fout = os.path.join(dirout_feature, "%s_%s.npy" % (a, b))
np.save(fout, pc)
del pc, pa, pb
if fo != None:
fo.close()
