def MongotoPTMannotation(proteinIDs, Tag_FTs, output_types, output_prefix):
table = functions.connectMongoDB('test', 'table')
entry = functions.connectMongoDB('uniprot', 'entry')
file = []
out_data = ''
if not os.path.exists(output_prefix):
os.makedirs(output_prefix)
for index, tag in enumerate(Tag_FTs):
file.append(open(output_prefix + '/' + tag + '.fasta', 'w'))
for id in proteinIDs:
ptm = table.find_one({'_id': id})
ft_index = []
print(ptm)
for index, ft in enumerate(Tag_FTs):
# ft = re.sub('[.]', '',ft) #take off .
unfold_ft = ft.split(" ")
for new_ft in unfold_ft:
if new_ft in ptm:
ft_index.extend(ptm[new_ft])
if len(ft_index) >= 1:
sequence = ptm['sequence']
if output_types == 1: #DUOLIN
out_data = duolin(ptm['_id'], ft_index, sequence)
else: #CHUNHUI
out_data = chunhui(ptm['_id'], sequence)
file[index].write(out_data)
for index, tag in enumerate(Tag_FTs):
file[index].close()
def main():
dbname = 'uniprot'
colname = 'table'
collection = functions.connectMongoDB(dbname, colname)
results = collection.find({})
display = {
'Phosphoserine': 0,
'Phosphothreonine': 0,
'Phosphotyrosine': 0,
'N6-acetyllysine': 0,
'Omega-N-methylarginine': 0,
'N6-methyllysine': 0,
'N6,N6-dimethyllysine': 0,
'N6,N6,N6-trimethyllysine': 0,
'N-linked(GlcNAc)asparagine': 0,
'S-palmitoylcysteine': 0,
'Pyrrolidonecarboxylicacid': 0,
'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-CterinSUMO)': 0
}
for data in results:
for ptm in display:
if ptm in data:
display[ptm] += len(data[ptm])
print(display)
with open('display.txt', 'w') as outfile:
json.dump(display, outfile)
def ptmPosition(Tag_FTs):
table = functions.connectMongoDB('uniprot', 'table')
out_data = ''
file = []
if not os.path.exists("data"):
os.makedirs("data")
for index, tag in enumerate(Tag_FTs):
file.append(open('data/' + tag + '.txt', 'w'))
with open("format8.txt") as fp:
for line in fp:
collapse = ' '.join(line.split())
parse = collapse.split(" ")
id = parse[1]
ptm = table.find_one({'_id': id})
ptm_pos = []
for index, ft in enumerate(Tag_FTs):
if ft in ptm:
ptm_pos.extend(ptm[ft])
relative_positions = calc_psition(int(parse[6]), int(parse[8]),
int(parse[9]), ptm_pos)
out_data = prepare(ptm['_id'], relative_positions)
file[index].write(out_data)
for index, tag in enumerate(Tag_FTs):
file[index].close()
def get_ids(sp):
ids = []
table = functions.connectMongoDB('uniprot', 'table')
cursor = table.find()
for doc in cursor:
if doc['species'] and sp in doc['species']:
ids.append(doc['_id'])
return ids
def ubiquitin(filepath,fts):
table = functions.connectMongoDB('uniprot','ubiquitinTable')
# Open a file
ac_flag = 0
out_ac = []
out_position = []
out_data = dict()
special = 0
specials = ['Glycyllysineisopeptide(Lys-Gly)','Peptide(Met-Gly)(interchainwithG-Cter','Glycylserineester(Ser-Gly)','Glycylcysteinethioester(Cys-Gly)']
with open(filepath) as fp:
for line in fp:
collapsed = ' '.join(line.split())
data = collapsed.split(";")
parsed_1 = data[0].split(" ")
if parsed_1[0] == "AC" and ac_flag == 0:
ac_flag = 1
out_ac.append(parsed_1[1])
if len(data) > 2:
for x in range(1, len(data)-1):
out_ac.append(data[x])
out_data = {'ac':out_ac}
##[go,interpro,pfam,prosite,smart,supfam]
elif parsed_1[0] == "FT":
if len(parsed_1) > 4 and special == 0:
ft = ''
for i in range(4,len(parsed_1)):
ft = ft + parsed_1[i]
ft = re.sub('[.]', '', ft)
out_position = functions.remove_duplicates([parsed_1[2],parsed_1[3]])
if ft in specials:
special = 1
continue
if ft in fts:
fts.setdefault(ft, []).append(out_position)
out_position = []
elif special == 1:
for i in range(1,len(parsed_1)):
ft = ft + parsed_1[i]
ft = re.sub('[.]', '', ft)
if ft in fts:
fts.setdefault(ft, []).append(out_position)
out_position = []
special = 0
elif parsed_1[0] == '//':
fts = dict( [(k,list(itertools.chain.from_iterable(v))) for k,v in fts.items() if len(v)>0]) #delete empty FTs from dictionary ##list(itertools.chain.from_iterable(v)) format
out_data = functions.merge_two_dicts(out_data,fts)
#print(out_data)
table.save(out_data)
fts = {'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-Cterinubiquitin)':[],'Glycylserineester(Ser-Gly)(interchainwithG-Cterinubiquitin)':[],
'Peptide(Met-Gly)(interchainwithG-Cterinubiquitin)':[],'Glycylcysteinethioester(Cys-Gly)(interchainwithG-Cterinubiquitin)':[]}
##rewind
out_ac = []
ac_flag = 0
out_position = []
fp.close()
def db_to_fasta(output_prefix):
entry = functions.connectMongoDB('uniprot', 'table')
out_data = ''
out_file = open(output_prefix + '.fasta', 'w')
entrys = entry.find({})
for doc in entrys:
out_data = prepareData(doc['_id'], doc['sequence'])
out_file.write(out_data)
out_file.close()
def main():
dbname = 'uniprot'
colname = 'ubiquitinTable'
collection = functions.connectMongoDB(dbname, colname)
write2file = []
takeoff = ['_id', 'ac']
##
with open('positionInfo.txt', 'w') as outfile:
for ac in acs:
result = collection.find_one({'ac': ac})
print(ac)
temp = {'AC': ac}
for output in result:
if output not in takeoff:
temp[output] = result[output]
write2file.append(temp)
json.dump(write2file, outfile)
def blast_output(output_prefix):
table = functions.connectMongoDB('uniprot', 'table')
if not os.path.exists(output_prefix):
os.makedirs(output_prefix)
out_file = open(output_prefix + '/input1.txt', 'w')
current = " "
with open("format8.txt") as fp:
for line in fp:
collapse = ' '.join(line.split())
parse = collapse.split(" ")
if current != parse[0]:
current = parse[0]
seq = get_query_seq(current)
q_id = '{:14}'.format(current)
out_file.write(q_id + seq + "\n")
pid = '{:14}'.format(parse[1])
p_doc = table.find_one({'_id': parse[1]})
p_seq = p_doc["sequence"]
start = int(parse[8]) - 1
end = int(parse[9])
p_seq = p_seq[start:end]
p_seq = fillup(int(parse[6]) - 1, p_seq)
out_file.write(pid + p_seq + "\n")
out_file.close()
def tableGeneration(filepath, fts):
table = functions.connectMongoDB('uniprot', 'table')
# Open a file
id_flag = 0
ac_flag = 0
out_ac = []
out_position = []
out_data = dict()
special = 0
sequence = ''
with open(filepath) as fp:
for line in fp:
collapsed = ' '.join(line.split())
data = collapsed.split(";")
parsed_1 = data[0].split(" ")
if parsed_1[0] == "ID" and id_flag == 0:
id_flag = 1
out_id = parsed_1[1]
elif parsed_1[0] == "AC" and ac_flag == 0:
ac_flag = 1
out_ac.append(parsed_1[1])
if len(data) > 2:
for x in range(1, len(data) - 1):
out_ac.append(data[x])
out_data = {'_id': out_id, 'ac': out_ac}
##[go,interpro,pfam,prosite,smart,supfam]
elif parsed_1[0] == "FT":
if len(parsed_1) > 4 and special == 0:
ft = ''
for i in range(4, len(parsed_1)):
ft = ft + parsed_1[i]
ft = re.sub('[.]', '', ft)
out_position = functions.remove_duplicates(
[parsed_1[2], parsed_1[3]])
if ft == 'Glycyllysineisopeptide(Lys-Gly)':
special = 1
continue
if ft in fts:
fts.setdefault(ft, []).append(out_position)
out_position = []
elif special == 1:
for i in range(1, len(parsed_1)):
ft = ft + parsed_1[i]
ft = re.sub('[.]', '', ft)
if ft in fts:
fts.setdefault(ft, []).append(out_position)
out_position = []
special = 0
##
## parse_1[0] is usually RT,DR,FT,or SQ etc... only squence part has length greater than 2
elif len(parsed_1[0]) > 2:
sequence += collapsed
elif parsed_1[0] == '//':
fts = dict(
[(k, list(itertools.chain.from_iterable(v)))
for k, v in fts.items() if len(v) > 0]
) #delete empty FTs from dictionary ##list(itertools.chain.from_iterable(v)) format
out_data = functions.merge_two_dicts(out_data, fts)
sequence = ''.join(sequence.split())
out_data['sequence'] = sequence
#print(out_data)
table.save(out_data)
fts = {
'Phosphoserine': [],
'Phosphothreonine': [],
'Phosphotyrosine': [],
'N6-acetyllysine': [],
'Omega-N-methylarginine': [],
'N6-methyllysine': [],
'N6,N6-dimethyllysine': [],
'N6,N6,N6-trimethyllysine': [],
'N-linked(GlcNAc)asparagine': [],
'S-palmitoylcysteine': [],
'Pyrrolidonecarboxylicacid': [],
'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-CterinSUMO)':
[],
'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-Cterinubiquitin)':
[]
}
##rewind
out_ac = []
id_flag = 0
ac_flag = 0
out_position = []
sequence = ''
fp.close()
def tableGeneration(filepath, ptms):
table = functions.connectMongoDB('uniprot', 'table')
table.drop()
out_id = ""
out_ac = []
out_position = []
out_data = dict()
sequence = ""
temp_ptm = ""
prev_fp_pos = 0
check = []
fp = open(filepath)
line = fp.readline()
while line:
collapsed = ' '.join(line.split())
data = collapsed.split(";")
info = data[0].split(" ")
tag = info[0]
#print(info[0]+" info1 "+info[1]+"\n")
if tag == "ID":
out_id = info[1]
elif tag == "AC":
out_ac.append(info[1])
if len(data) > 2:
for x in range(1, len(data) - 1):
out_ac.append(data[x].lstrip())
elif tag == "OC":
check.append(info[1].lstrip())
if len(data) > 2:
for x in range(1, len(data) - 1):
check.append(data[x].lstrip())
out_data = {"_id": out_id, "ac": out_ac, "species": check}
elif tag == "FT":
temp_ptm = ""
out_position = functions.remove_duplicates([info[2], info[3]])
temp_ptm = " ".join(info[4:])
#if "Q9TT90" in out_ac:
# print("################temp_ptm is 1 "+temp_ptm+"\n")
prev_fp_pos = fp.tell()
line = ' '.join(fp.readline().split())
info = line.split(" ")
while info[0] == "FT":
if len(info) > 3 and is_number(info[2]) and is_number(info[3]):
#if "Q9TT90" in out_ac:
# print("###########temp_ptm is 2 "+temp_ptm+"\n")
temp_ptm = re.sub('(\.*)\)', ')', temp_ptm)
for doc in ptms:
#if "Q9TT90" in out_ac and doc == 'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-CterinSUMO)':
# print(doc+" vs "+re.sub('[\.|\;].*','',temp_ptm)+"\n")
if doc == re.sub('[\.|\;].*', '', temp_ptm):
#if "Q9TT90" in out_ac:
# print("yes\n")
ptms.setdefault(doc, []).append(out_position)
temp_ptm = ""
out_position = functions.remove_duplicates(
[info[2], info[3]])
temp_ptm = " ".join(info[4:])
else:
temp_ptm = temp_ptm + " ".join(info[1:])
#if "Q9TT90" in out_ac:
# print("#################temp_ptm is 3 "+temp_ptm+"\n")
#for i in range(1,len(info)):
# temp_ptm += info[i].rstrip()
#print(temp_ptm+"\n")
prev_fp_pos = fp.tell()
line = ' '.join(fp.readline().split())
info = line.split(" ")
temp_ptm = re.sub('(\.*)\)', ')', temp_ptm)
for doc in ptms:
#if "Q9TT90" in out_ac and doc == 'Glycyllysineisopeptide(Lys-Gly)(interchainwithG-CterinSUMO)':
# print(doc+" vs "+re.sub('[\.|\;].*','',temp_ptm)+"\n")
if doc == re.sub('[\.|\;].*', '', temp_ptm):
#if "Q9TT90" in out_ac:
# print("yes\n")
ptms.setdefault(doc, []).append(out_position)
ptms = dict([(k, list(itertools.chain.from_iterable(v)))
for k, v in ptms.items() if len(v) > 0])
fp.seek(prev_fp_pos)
elif tag == "SQ":
sequence = seq_read(fp)
out_data = functions.merge_two_dicts(out_data, ptms)
out_data['sequence'] = sequence
table.save(out_data)
##rewind
ptms = {
'Phosphoserine': [],
'Phosphothreonine': [],
'Phosphotyrosine': [],
'N6-acetyllysine': [],
'Omega-N-methylarginine': [],
'Dimethylated arginine': [],
'Symmetric dimethylarginine': [],
'Asymmetric dimethylarginine': [],
'N6-methyllysine': [],
'N6,N6-dimethyllysine': [],
'N6,N6,N6-trimethyllysine': [],
'N-linked (GlcNAc) asparagine': [],
'S-palmitoyl cysteine': [],
'Pyrrolidone carboxylic acid': [],
'Glycyl lysine isopeptide (Lys-Gly)(interchain with G-Cter in SUMO)':
[],
'Glycyl lysine isopeptide (Lys-Gly)(interchain with G-Cter in ubiquitin)':
[]
}
out_data.clear()
out_ac = []
out_position = []
sequence = ""
check = []
line = fp.readline()
fp.close()
def blast_output(filepath,ptms,out_folder):
"""
main function to generate display from blast output
and write to files
"""
file = []
for ptm in ptms:
file.append(open(out_folder+'/'+ptm+'.txt','w'))
table = functions.connectMongoDB('uniprot','table')
out_file = open(out_folder+'/blast_output.txt','w')
seqs_start_position = 0
seqs_end_position = 0
output = dict()
ac_deletions = dict()
insertions = dict()
ab_ptms = dict()
fp = open(filepath)
line = fp.readline()
sequence_pad = -1
while line:
collapsed = ' '.join(line.split())
data = collapsed.split(" ")
tag = data[0]
# 1. read blast result sequences
if tag == 'Query_1': #blast result start
sequence_pad += 1
temp_q_end = int(data[3])
q_seq = data[2]
seqs_start_position = line.find(data[2]) # start position in txt
seqs_end_position = line.find(data[3]) - 2 # end position in txt
seqs_end_index = dict() # sequence end index
seqs_start_index = dict() # sequence start index
line = fp.readline()
collapsed = ' '.join(line.split())
data = collapsed.split(" ")
prev_ac = ""
while line and data[0] != "Lambda":
if data[0] == 'Query_1': # if its query
sequence_pad += 1
seqs_start_position = line.find(data[2])
seqs_end_position = line.find(data[3]) - 2
if temp_q_end == int(data[1])-1:
temp_q_end = int(data[3])
q_seq += data[2]
else:
print("special case!")
elif len(data) == 4 and is_int(data[1]) and is_int(data[3]): # if its subjects
if data[0] in output: # if its not head
prev_ac = data[0]
seqs_end_index[data[0]] = int(data[3])
output[data[0]] += line[seqs_start_position:seqs_end_position]
else: # if its head
prev_ac = data[0]
seqs_start_index[data[0]] = int(data[1])
seqs_end_index[data[0]] = int(data[3])
output[data[0]] = reposition_seq(line[seqs_start_position:seqs_end_position],sequence_pad)
elif data[0] == '\\':
if prev_ac in ac_deletions:
delete = get_deletions(fp,sequence_pad)
ac_deletions[prev_ac] += delete
else:
delete = get_deletions(fp,sequence_pad)
ac_deletions[prev_ac] = delete
line = fp.readline()
collapsed = ' '.join(line.split())
data = collapsed.split(" ")
##########check ptms
#for id in ids:
# temp = table.find_one({"_id": id})
# for ptm in ptms:
# if ptm in temp:
# print(temp[ptm])
##################
# preprocess data
for id in output:
output[id] = output[id].ljust(len(q_seq))
output[id] = output[id].replace(" ",".")
insertions[id] = get_inserts(output[id])
dict((k, v) for k, v in insertions.iteritems() if v)
#############check deletions
#for i in ac_deletions:
# for j in ac_deletions[i]:
# print("id: "+i+"\tpos: "+str(j.pos)+"\tseq: "+j.seq)
#####################
# ptm position is relative to the line in the file not sequence now
for counter, ptm in enumerate(ptms):
# generate the ptm position for display
ab_ptms = get_ptms(ptm,table,seqs_start_index,seqs_end_index,insertions,ac_deletions,output) #TODO check if ids are right
display_ptm(ab_ptms,file[counter],output) #TODO one more ids
identities = get_identities(out_folder)
display_output(q_seq,output,identities,out_file) #TODO ids here
line = fp.readline()
out_file.close()
fp.close()
for index, ptm in enumerate(ptms):
file[index].close()