def generateSomeSpeciesLists(ftmp, fnontmp, species='MYCPN'):
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': False, 'accession': True}
docs = do.QueryObj({
"keyword.@id": 'KW-0812',
'_id': {
'$regex': species
}
},
projection=projection)
tmplist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
docs = do.QueryObj(
{
"keyword.@id": {
'$ne': 'KW-0812'
},
'keyword': {
'$exists': True
},
'_id': {
'$regex': 'HUMAN'
}
},
projection=projection)
nontmplist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
print('query %d tmp and %d nontmp' % (len(tmplist), len(nontmplist)))
saveList(tmplist, ftmp)
saveList(nontmplist, fnontmp)
return tmplist, nontmplist
def save(aclist, dbnam, fnotSave=None):
# aclist = ['P06685', 'P06686']
# dbnam = 'seqtmppi_test1'
do_all = DataOperation('uniprot', 'seqtmppi_positive')
do_new = DataOperation('uniprot', dbnam)
notsaveCount = 0
notsaveList = []
for ac in aclist:
protein = queryProtein(ac, do_all)
if protein == None:
print('not save protein %s' % ac)
continue
# projection = {'_id': True, 'sequence.@length': True, 'sequence.#text': True, 'keyword.@id': True,
# 'comment.subcellularLocation.location': True}
# protein_ens = ensomblePortein(queryProtein(ac, do_all,projection=projection))
# protein_ens['accession'] = ac
# protein['ensomble'] = protein_ens
result = do_new.UpSertOne({'accession': ac}, protein)
if result.matched_count != 0:
print('not save %s' % ac)
notsaveCount = notsaveCount + 1
notsaveList.append(ac)
print('not save %d' % (notsaveCount))
if fnotSave:
saveList(notsaveList, fnotSave)
return notsaveList
def generateCoQLists(fcoQ):
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True, 'accession': True}
docs = do.QueryObj({"keyword.@id": 'KW-0830'}, projection=projection)
coQlist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
print('query %d coQ' % (len(coQlist)))
saveList(coQlist, fcoQ)
return coQlist
def generateCoQInfo(finfo):
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True, 'accession': True}
docs = do.QueryObj({"keyword.@id": 'KW-0830'}, projection=projection)
coQinfo = [
(x['accession'][0],
x['_id'].split('_')[1]) if isinstance(x['accession'], list) else
(x['accession'], x['_id'].split('_')[1]) for x in docs
]
print('query %d coQ info' % (len(coQinfo)))
saveList(coQinfo, finfo)
return coQinfo
def findKeyProtein(fin, fout, keyword):
# keyword = 'KW-0297'
tmplist = readIDlist(fin)
GPCRlist = []
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True}
for ac in tmplist:
dic = {'accession': ac, "keyword.@id": keyword}
result = do.QueryObj(dic, projection=projection)
for r in result:
GPCRlist.append(ac)
print(r)
saveList(GPCRlist, fout)
def getALlGprotein(fout):
# {$or:[
# {"protein.recommendedName.fullName":{$regex:/G protein +/}},
# {"protein.recommendedName.fullName":{$regex:/G protein-coupled receptor +/}},
# {"protein.alternativeName.fullName":{$regex:/G protein +/}},
# {"protein.alternativeName.fullName":{$regex:/G protein-coupled receptor +/}}
# ]}
GPCRlist = []
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {
'_id': True,
'protein.recommendedName.fullName': True,
'protein.alternativeName.fullName': True
}
count = 0
dic = {
# 'accession': ac,
'$or': [{
"protein.recommendedName.fullName": {
'$regex': 'G protein '
}
}, {
"protein.recommendedName.fullName": {
'$regex': 'Guanine nucleotide-binding protein'
}
}, {
"protein.alternativeName.fullName": {
'$regex': 'G protein '
}
}, {
"protein.alternativeName.fullName": {
'$regex': 'Guanine nucleotide-binding protein'
}
}]
}
result = do.QueryObj(dic, projection=projection)
for r in result:
count = count + 1
GPCRlist.append(((r['_id'], [
x for x in handleSubcelluarLeaf(
r['protein'],
keys=['alternativeName', 'recommendedName', 'fullName'])
])))
print(((r['_id'], [
x for x in handleSubcelluarLeaf(
r['protein'],
keys=['alternativeName', 'recommendedName', 'fullName'])
])))
saveList(GPCRlist, fout)
def getallProtein():
'''
dao
:param AC:
:param do:
:return:
'''
do = DataOperation(db_name, table_target)
projection = {'_id': True, 'UNIPROID':True}
docs = do.GetALL(projection=projection,limit=0)
for protein in docs:
if protein['UNIPROID'] == '':continue
for pro in multiSplit(protein['UNIPROID']):
yield pro.strip()
def funcPfam(x):
# ac = 'P03372'
do = DataOperation('uniprot', 'uniprot_sprot')
result = queryPfam(x[0], do, tophit=True)
x[1] = result[0]
x[2] = result[1]
return x
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 getSingleInfo(fin, fout, fin_type='single', col=[0, 1]):
if fin_type == 'pair':
df = pd.read_table(fin, header=None)[col]
dat = df.to_numpy().reshape(1, -1)
proteins = set(dat[0])
elif fin_type == 'single':
proteins = readIDlist(fin)
else:
pass
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {
'_id': True,
'sequence.@length': True,
'sequence.#text': True,
'keyword.@id': True,
'comment.subcellularLocation.location': True
}
prod = Protein()
with open(fout, 'w') as fo:
for AC in proteins:
pro = queryProtein(AC, do, projection=projection)
pro['accession'] = AC
if not prod.checkProtein(
pro['sequence']['#text'], 50, 2000, uncomm=True):
continue
proinfo = ensomblePortein(pro)
for v in proinfo.values():
fo.write(str(v))
fo.write('\t')
fo.write('\n')
fo.flush()
def getallProtein(fout):
'''
dao
:param AC:
:param do:
:return:
'''
do = DataOperation('DrugKB', 'protein')
projection = {'_id': True, 'accession': True}
# one accession mapping several protein sequence
docs = do.GetALL(projection=projection, limit=0)
proteinlist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
saveList(proteinlist, fout)
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 getTmp(fin, fout):
'''
:param fin: protein list
:param fout: tmp list
:return:
'''
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True, 'keyword.@id': True}
aclist = readIDlist(fin)
with open(fout, 'w') as fo:
for AC in aclist:
qa = do.QueryOne('accession', AC, projection=projection)
if qa == None: continue
if checkTaN(qa['keyword']):
print('%s TMP' % AC)
pa_TMP_flag = False if 'keyword' not in qa.keys() else checkTaN(
qa['keyword'])
if pa_TMP_flag:
fo.write('%s\n' % AC)
fo.flush()
def test_queryProtein(self):
do = DataOperation('uniprot', 'uniprot_sprot')
AC = 'P34397'
protein = None
# one accession mapping several protein sequence
projection = {
'_id': True,
'sequence.@length': True,
'sequence.#text': True,
'keyword.@id': True,
'comment.subcellularLocation.location': True
}
docs = do.Query('accession', AC, projection=projection)
count = 0
for doc in docs:
count = count + 1
if count > 1:
# 一个accession 查询到多个蛋白质
# 保存这个列表
print('%s is more than one entry' % AC)
protein = doc
protein['accession'] = AC
ensomblePortein(protein)
def findGProtein(fin, fout):
# {"protein.recommendedName.fullName":{$regex:/Guanine nucleotide-binding protein*/}}
# keyword = 'KW-0297'
tmplist = readIDlist(fin)
GPCRlist = []
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True}
count = 0
for ac in tmplist:
dic = {
'accession':
ac,
'$or': [{
"protein.recommendedName.fullName": {
'$regex': 'G protein '
}
}, {
"protein.recommendedName.fullName": {
'$regex': 'Guanine nucleotide-binding protein'
}
}, {
"protein.alternativeName.fullName": {
'$regex': 'G protein '
}
}, {
"protein.alternativeName.fullName": {
'$regex': 'Guanine nucleotide-binding protein'
}
}]
}
result = do.QueryObj(dic, projection=projection)
for r in result:
count = count + 1
GPCRlist.append(ac)
print(count, r)
saveList(GPCRlist, fout)
def generateCriterLists(ftmp, fnontmp):
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': False, 'accession': True}
docs = do.QueryObj(
{
"keyword.@id": 'KW-0812',
'comment.subcellularLocation.location.#text': {
'$exists': True
}
},
projection=projection)
tmplist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
docs = do.QueryObj(
{
"keyword.@id": {
'$ne': 'KW-0812'
},
'keyword': {
'$exists': True
},
'comment.subcellularLocation.location.#text': {
'$exists': True
}
},
projection=projection)
nontmplist = [
x['accession'][0]
if isinstance(x['accession'], list) else x['accession'] for x in docs
]
print('query %d tmp and %d nontmp' % (len(tmplist), len(nontmplist)))
saveList(tmplist, ftmp)
saveList(nontmplist, fnontmp)
return tmplist, nontmplist
def getFasta(fin_all_protein, fout):
proteins = readIDlist(fin_all_protein)
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'sequence.#text': True}
with open(fout, 'w') as fo:
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
records = []
for AC in proteins:
pro = queryProtein(AC, do, projection=projection)
if not pro: continue
record = SeqRecord(Seq(pro['sequence']['#text']),
id=AC,
description='')
records.append(record)
#fo.write('>%s\n%s\n'%(AC,pro['sequence']['#text']))
#fo.flush()
SeqIO.write(records, fout, 'fasta')
from DatabaseOperation2 import DataOperation
from ProteinDealer import Protein
from dao import queryProtein, ensomblePortein
import time
if __name__ == '__main__':
print('start', time.strftime('%Y-%m-%d %H:%M:%S', time.localtime()))
start = time.time()
pa = 'Q14118'
projcetion = {'dbReference.text':True,'_id':False}
dic = {'accession':pa,'dbReference.@type':'pfam'}
do = DataOperation('uniprot', 'uniprot_sprot')
qa = do.QueryObj(dic,projcetion= projcetion)
dbReference = qa['dbReference']
subcellularLocations = []
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {'_id': True, 'sequence.@length': True, 'sequence.#text': True, 'keyword.@id': True,
'comment.subcellularLocation.location': True}
AC = 'P82432'
pro = queryProtein(AC, do, projection=projection)
pro['accession'] = AC
proinfo = ensomblePortein(pro)
pass
print('stop', time.strftime('%Y-%m-%d %H:%M:%S', time.localtime()))
print('time', time.time() - start)
def proteinPfam(fin,fout,tophit=True,item='Pfam'):
do = DataOperation('uniprot', 'uniprot_sprot')
df = pd.read_csv(fin, header=None)
df = pd.DataFrame(df)
df2 = df.apply(lambda x: funcPfam(x,do,tophit=tophit,item=item), axis=1)
df2.to_csv(fout, sep='\t',header=None, index=None)
for q in qa:
dbReference = q['dbReference']
# {'@type': 'Pfam', '@id': 'PF18424', 'property': [{'@type': 'entry name', '@value': 'a_DG1_N2'}
# {'@type': 'Pfam', '@id': 'PF12743', 'property': [{'@type': 'entry name', '@value': 'ESR1_C'}, {'@type': 'match status', '@value': '1'}]}
result = getPfam(dbReference)
return result if not tophit else result[0]
def addProteinPfam():
pass
def funcPfam(x):
return x
if __name__ == '__main__':
do = DataOperation('uniprot', 'uniprot_sprot')
projection = {
'_id': True,
'sequence.@length': True,
'sequence.#text': True,
'keyword.@id': True,
'comment.subcellularLocation.location': True
}
AC = 'Q13206'
pro = queryProtein(AC, do, projection=projection)
pro['accession'] = AC
proinfo = ensomblePortein(pro)