def harmonizeMIRNA(mirna):
"""
:param mirna:
:return: tries to return a normalized name ...
9761 microRNA
7958 MicroRNA
2311 MiRNA
2191 miRNA
1844 hsa
1440 let
578 miRNAS
437 MICRORNA
299 microRNAS
256 MIRNA
155 mmu
125 Micro
116 micro
"""
possibleOrgStarts = ['mmu', 'hsa']
recOrg = None
for x in possibleOrgStarts:
if mirna.startswith(x + "-"):
recOrg = x
mirna = mirna.replace(x + "-", "", 1)
break
possibleStarts = [
'microRNA', 'MicroRNA', 'MiRNA', 'miRNA', 'MICRORNA', 'microRNA',
'MIRNA'
]
for x in possibleStarts:
if mirna.startswith(x + "-"):
mirna = mirna.replace(x, "miR", 1)
break
try:
oMirna = miRNA(mirna)
mirna = oMirna.getStringFromParts(
[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR])
except:
pass
return (recOrg, mirna)
def handleHarmonizedNameMirna(x):
idx = x.synonym.syns.index(x.hitSyn)
if idx >= 0:
try:
test = miRNA(x.synonym.syns[idx])
outstr = test.getStringFromParts([
miRNAPART.ORGANISM, miRNAPART.MATURE, miRNAPART.ID,
miRNAPART.PRECURSOR, miRNAPART.MATURE_SEQS, miRNAPART.ARM
],
normalized=True)
return outstr
except:
# sys.stderr.write("cannot parse mirna: " + x.synonym.syns[idx])
if __debug__:
pass
# miRNA(x.synonym.syns[idx])
# exit(-1)
for mirnaSyn in x.synonym.syns:
if mirnaSyn.startswith("miR-") and not 'mediated' in mirnaSyn:
test = miRNA(mirnaSyn)
outstr = test.getStringFromParts([
miRNAPART.ORGANISM, miRNAPART.MATURE, miRNAPART.ID,
miRNAPART.PRECURSOR, miRNAPART.MATURE_SEQS, miRNAPART.ARM
],
normalized=True)
return outstr
if __debug__:
print("Could not match", x.hitSyn)
return None
def processFile(fin, org):
foundRels = defaultdict(list)
for line in fin:
line = line.strip().split("\t")
# miR-29-b Mir-29b MIRNA GRN PGRN GENE 20479936 True True [('12', '1V2', 'NEG', 'downregulat', '20479936.2.4', False, (0, 7), (74, 78), (8, 21), 'all_rels', 1, 1, 2, 0)]
mirna = line[0]
gene = line[3]
docid = line[6]
evs = eval(line[9])
if gene in normGeneSymbols:
gene = normGeneSymbols[gene]
elif gene.upper() in normGeneSymbols:
gene = normGeneSymbols[gene.upper()]
for ev in evs:
relAcc = ev[-4] != 0 or ev[-3] != 0 or ev[-2] != 0
if relAcc:
try:
rel = {
'mirna':
miRNA(mirna).getStringFromParts([
miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR
]),
'gene':
gene,
'docid':
docid,
'org':
org
}
foundRels[docid].append(rel)
except:
continue
return foundRels
def loadFromFile(cls, infile="/mnt/c/ownCloud/data/miRExplore/obodir/mirnas_mirbase.csv"):
retDB = MI2Mirna()
with open(infile, 'r') as fin:
for line in fin:
line = line.strip()
if len(line) == 0:
continue
line = line.split("\t")
miID = line[0]
mirna = line[1]
if not (mirna.startswith("mmu") or mirna.startswith("hsa")):
continue
try:
miObj = miRNA(mirna)
miNum = miObj.getPart(miRNAPART.ID, None)
if miNum == None:
continue
org = mirna[0:3]
retDB.mi2mirna[miID] = miNum
retDB.mirnaNum2mi[(org, miNum)] = miID
except:
continue
return retDB
def getOrgMIRNAID(mirnaid, listedIDs, prefix, getID):
mirna = miRNA(matureID1)
idPart = getID(mirna)
if idPart == None:
print("no ID! " + matureID1)
return None
idPart = idPart.upper()
idpartIdx = -1
if idPart in listedIDs:
idpartIdx = listedIDs.index(idPart)
else:
idpartIdx = len(listedIDs)
listedIDs.append(idPart)
synid = prefix + str(idpartIdx)
return (synid,listedIDs)
'miR-23a-3p', 'miR-338-3p', 'miR-103-3p', 'miR-362-3p',
'let-7g-5p', 'miR-155-5p', 'miR-140-5p', 'miR-122-5p', 'miR-22-3p',
'miR-3470a', 'let-7d-5p'
]
}
ti = 0
for x in interactions:
ti += len(interactions[x])
print("Total Interactions", ti)
for gene in interactions:
mirlist = interactions[gene]
mirids = [miRNA(x) for x in mirlist]
interactions[gene] = mirids
graph = nx.Graph()
foundInteractions = defaultdict(set)
graphConnections = defaultdict(list)
saseRels = 0
def loadTextmining(path):
global saseRels
with open(path, 'r') as fin: #/tmp/mirtex/mirel_sase_new
# number of genes with interaction
allGenes = set()
for rdb in relDBs:
allGenes = allGenes.union(set(rdb.all_ltypes))
print("Number of genes with interaction", len(allGenes))
# number of miRNAs with interaction
## restrict to miR-x
allMirnas = set()
for rdb in relDBs:
for mirna in rdb.all_rtypes:
try:
mirObj = miRNA(mirna)
allMirnas.add(
mirObj.getStringFromParts(
[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR]))
except:
print(mirna)
exit(-1)
print("Number of mirnas with interaction", len(allMirnas))
# number of gene-mirna interactions with disease association
distinctInteractionsWithDisease = set()
interactionsWithDisease = set()
def fetchGenes(cls,
requestDict,
gene2name=None,
minPMIDEvCount=0,
minTgtCount=0,
MIRNASTRPARTS=[miRNAPART.MATURE, miRNAPART.ID],
acceptEv=None,
verbose=False):
jsonRes = cls.fetchSimple(requestDict)
graph = networkx.Graph()
if verbose:
print(len(jsonRes['rels']))
nodeCounter = Counter()
allGenes2Name = {}
if gene2name != None:
for gene in gene2name:
for elem in gene2name[gene]:
allGenes2Name[elem.upper()] = gene
targets2sources = defaultdict(set)
edge2datasourceCount = defaultdict(lambda: Counter())
edge2celltypes = defaultdict(set)
edge2celltypePMID = defaultdict(lambda: defaultdict(set))
for rel in jsonRes['rels']:
source = rel['lid']
target = rel['rid']
if gene2name != None:
if source.upper() in allGenes2Name:
source = allGenes2Name[source.upper()]
if target.upper() in allGenes2Name:
target = allGenes2Name[target.upper()]
try:
target = miRNA(target)
target = target.getStringFromParts(MIRNASTRPARTS,
normalized=True)
except:
pass
edge = (source, target)
for ev in rel['evidences']:
ds = ev['data_source']
if acceptEv != None:
evRes = acceptEv(ev)
else:
evRes = True
if evRes:
edge2datasourceCount[edge][ds] += 1
if ds in ["pmid"]:
docid = ev["docid"]
allCellEvs = jsonRes['pmidinfo'].get("cells", {}).get(
docid, None)
if allCellEvs != None:
for cellEv in allCellEvs:
cellInfo = (cellEv['termid'],
cellEv['termname'])
if cellInfo[1].lower() in [
'cell', 'protein', 'has', 'signaling',
'function', 'role', 'sfswt-1', 'has-15'
]:
continue
if not cellInfo[0].startswith(
"CL"
): # and not cellInfo[0].startswith("CVCL"):
continue
if not docid in jsonRes['pmidinfo']['disease']:
continue
edge2celltypes[edge].add(cellInfo)
edge2celltypePMID[edge][cellInfo].add(docid)
targets2sources[target].add(source)
for rel in jsonRes['rels']:
source = rel['lid']
target = rel['rid']
if gene2name != None:
if source.upper() in allGenes2Name:
source = allGenes2Name[source.upper()]
if target.upper() in allGenes2Name:
target = allGenes2Name[target.upper()]
if target.upper().startswith("MIR") or target.upper().startswith(
"LET"):
try:
target = miRNA(target)
target = target.getStringFromParts(MIRNASTRPARTS,
normalized=True)
except:
pass
elif source.upper().startswith("MIR") or source.upper().startswith(
"LET"):
try:
source = miRNA(source)
source = source.getStringFromParts(MIRNASTRPARTS,
normalized=True)
except:
pass
edge = (source, target)
edgeCounts = edge2datasourceCount[edge]
allEvCount = sum([1 for x in edgeCounts])
otherEvCount = sum([1 for x in edgeCounts if x != "pmid"])
if allEvCount == 0:
if verbose:
print("Removing edge", edge, "for 0 count")
continue
if otherEvCount == 0 and edge2datasourceCount[edge][
"pmid"] < minPMIDEvCount:
continue
if len(targets2sources[target]) < minTgtCount:
continue
graph.add_node(source, color='red')
graph.add_node(target, color='blue')
graph.add_edge(source,
target,
celldata=edge2celltypes[edge],
cellEvidence=edge2celltypePMID[edge])
nodeCounter[source] += 1
nodeCounter[target] += 1
return graph, nodeCounter, edge2datasourceCount, jsonRes
def findCooccurrences(pubmed, hgncHits, mirnaHits, sentDB):
def checkSynHit(synhit):
if len(synhit.foundSyn) <= 5:
return synhit.perfectHit == True
return True
def chekSynHitMirna(synhit):
if len(synhit.foundSyn) <= 5:
foundSyn = synhit.foundSyn.lower()
return foundSyn.startswith('mir') or foundSyn.startswith('micro')
return True
setAllGenes = set([x for x in hgncHits if checkSynHit(x)])
setAllMirnas = set([x for x in mirnaHits if chekSynHitMirna(x)])
hgncBySent = defaultdict(list)
mirnaBySent = defaultdict(list)
hgncToSent = {}
mirnaToSent = {}
for hit in hgncHits:
parSenID = (hit.documentID.parID, hit.documentID.senID)
hgncBySent[parSenID].append(hit)
hgncToSent[hit] = parSenID
for hit in mirnaHits:
parSenID = (hit.documentID.parID, hit.documentID.senID)
mirnaBySent[parSenID].append(hit)
mirnaToSent[hit] = parSenID
allCoocs = []
for x in setAllMirnas:
for y in setAllGenes:
foundCooc = Cooccurrence()
foundCooc.pubmed = pubmed
if re.match('MIPF[0-9]+', x.synonym.id) != None:
foundCooc.idtype = "MIRNA_FAMILY"
elif re.match('MIMAT[0-9]+', x.synonym.id) != None:
foundCooc.idtype = "MIRNA"
elif re.match('MI[0-9]+', x.synonym.id) != None:
foundCooc.idtype = 'MIRNA_PRE'
elif re.match('ORGMIR[0-9]+', x.synonym.id) != None:
foundCooc.idtype = 'MIRNA_ORGMIR'
elif re.match('ORGMI[0-9]+', x.synonym.id) != None:
foundCooc.idtype = 'MIRNA_ORGMIR'
else:
foundCooc.idtype = 'UNKNOWN'
foundCooc.gene = y.synonym.id
foundCooc.mirna = x.synonym.id
foundCooc.mirnadesc = str(x.synonym)
foundCooc.mirnaFound = x.hitSyn
idx = x.synonym.syns.index(x.hitSyn)
foundCooc.mirnaFound = None
if idx >= 0:
try:
test = miRNA(x.synonym.syns[idx])
outstr = test.getStringFromParts([
miRNAPART.ORGANISM, miRNAPART.MATURE, miRNAPART.ID,
miRNAPART.PRECURSOR, miRNAPART.MATURE_SEQS,
miRNAPART.ARM
],
normalized=True)
foundCooc.mirnaFound = outstr
except:
print("cannot parse mirna ", x.synonym.syns[idx])
sys.stderr.write("cannot parse mirna: " +
x.synonym.syns[idx])
if __debug__:
miRNA(x.synonym.syns[idx])
exit(-1)
foundCooc.mirnaFound = None
if idx < 0 or foundCooc.mirnaFound == None:
for mirnaSyn in x.synonym.syns:
if mirnaSyn.startswith(
"miR-") and not 'mediated' in mirnaSyn:
test = miRNA(mirnaSyn)
outstr = test.getStringFromParts([
miRNAPART.ORGANISM, miRNAPART.MATURE, miRNAPART.ID,
miRNAPART.PRECURSOR, miRNAPART.MATURE_SEQS,
miRNAPART.ARM
])
foundCooc.mirnaFound = outstr
break
if True and pubmed == '21682933':
print(pubmed)
miRNALoc = mirnaToSent[x]
hgncLoc = hgncToSent[y]
if miRNALoc[0] == hgncLoc[0]:
foundCooc.sameParagraph = True
if miRNALoc[1] == hgncLoc[1]:
foundCooc.sameSentence = True
foundCooc.relation = findRelation(x, y, sentDB)
allCoocs.append(foundCooc)
return allCoocs
for geneName in ["MEG3", "NEAT1","MMP2", "MMP9", "MMP12"]:
requestData = {}
requestData['gene'] = [geneName]
requestData['sentences'] = "false"
#print(requestData)
_,_,_, json = DataBasePlotter.fetchGenes(requestData, gene2name=None, minPMIDEvCount=0, minTgtCount=0, acceptEv=acceptEvidence, MIRNASTRPARTS=[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR])
for x in json["rels"]:
mirnastr = x["rid"]
omir = miRNA(mirnastr)
simpleStr = omir.getStringFromParts(miRNACOMPARISONLEVEL.PRECURSOR.value)
if simpleStr == "miR-7":
simpleStr = "let-7"
#print(x["lid"], x["rid"], simpleStr)
gene2result[geneName].add(simpleStr)
for ev in x["evidences"]:
if "docid" in ev:
rel2docs[(geneName, simpleStr)].add((ev["docid"], ev["data_source"]))
else:
rel2docs[(geneName, simpleStr)].add(ev["data_source"])
'miR-16-1-3p', 'miR-882', 'miR-497-5p', 'miR-26a-5p', 'miR-124-3p',
'miR-26b-5p', 'miR-5620-3p', 'mIR-19a-3p', 'miR-130a-3p',
'miR-690', 'miR-185-5p', 'miR-31-5p', 'miR-340-5p', 'miR-1843-5p',
'miR-466f-3p', 'miR-301a-3p', 'miR-101a-3p', 'miR-210-3p',
'miR-107-3p', 'miR-706', 'miR-23b-3p', 'miR-146a-5p', 'miR-467f',
'miR-322-5p', 'miR-15a-5p', 'miR-29b-1-5p', 'let-7e-5p',
'miR-23a-3p', 'miR-338-3p', 'miR-103-3p', 'miR-362-3p',
'let-7g-5p', 'miR-155-5p', 'miR-140-5p', 'miR-122-5p', 'miR-22-3p',
'miR-3470a', 'let-7d-5p'
]
}
for gene in interactions:
mirlist = interactions[gene]
mirids = [miRNA(x) for x in mirlist]
interactions[gene] = mirids
graph = nx.Graph()
foundInteractions = defaultdict(set)
pickleFile = '/home/mjoppich/chemokines.upd.graph.pickle'
if os.path.isfile(pickleFile):
with open(pickleFile, 'rb') as infile:
graphConnections = pickle.load(infile)
else:
test = InteractionRetriever(
elemsByGene = defaultdict(lambda: defaultdict(set))
allMirna = set(networks[network])
miStr2mirna = {}
allTargetMirna = []
mirnaObj2str = {}
mirna2evs = defaultdict(set)
newAllMirna = set()
for x in allMirna:
try:
oMirna = miRNA(x)
allTargetMirna.append(oMirna)
miStr = oMirna.getStringFromParts(
[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR])
miStr2mirna[miStr] = oMirna
mirnaObj2str[oMirna] = miStr
newAllMirna.add(miStr)
except:
pass
allMirna = newAllMirna
#allMirna = set([str(x) for x in allTargetMirna])
matureAcc1 = None
matureID1 = None
matureAcc2 = None
matureID2 = None
MIid = mirnaAccession = row['Accession']
matureAcc1 = row['Mature1_Acc']
matureID1 = row['Mature1_ID']
matureID2 = row['Mature2_ID']
matureAcc2 = row['Mature2_Acc']
if not (matureAcc1 == None or matureAcc1 == 'None'):
MIMAT2MIRNA[matureAcc1] = miRNA(matureID1)
MI2MIMAT[MIid].add(matureAcc1)
if not (matureAcc2 == None or matureAcc2 == 'None'):
MIMAT2MIRNA[matureAcc2] = miRNA(matureID2)
MI2MIMAT[MIid].add(matureAcc2)
def makeFamilySynonymes():
vFamSyns = []
for family in familyDB:
for (miID, miName) in family.childMIMATs:
interactions = networks[network]
acceptedInteractions = defaultdict(set)
typeByGene = defaultdict(lambda: Counter())
elemsByGene = defaultdict(lambda: defaultdict(set))
allMirna = set()
miStr2mirna = {}
normalizedInteractions = defaultdict(set)
for gene in interactions:
for mirna in interactions[gene]:
try:
oMirna = miRNA(mirna)
mirnaN = oMirna.getStringFromParts(
[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR])
mirna = mirnaN
except:
pass
allMirna.add(mirna)
normalizedInteractions[gene].add(mirna)
allTargetMirna = []
for x in allMirna:
try:
def hfi_general():
interactReq = request.get_json(force=True, silent=True)
if interactReq == None:
return app.make_response((jsonify({'error':
'invalid json'}), 400, None))
entType = interactReq.get('type', "gene")
if not entType.upper() in ['GENE', 'MIRNA']:
return app.make_response(
(jsonify({'error': 'invalid enttity type ' + entType}), 400, None))
mirnas = []
genes = []
if entType.upper() == 'GENE':
entName = interactReq.get('name', None)
if entName != None:
genes.append(entName)
elif entType.upper() == 'MIRNA':
entName = interactReq.get('name', None)
if entName != None:
mirnas.append(entName)
if all([len(x) == 0 for x in [mirnas, genes]]):
return app.make_response(
(jsonify({'error': 'no entity names given'}), 400, None))
relObj = returnInteractions(genes, mirnas, None, loadSentences=False)
rels = relObj['rels']
seenInteractors = defaultdict(set)
seenPMIDs = set()
seenEvidenceTypes = Counter()
for rel in rels:
"""
allrels.append({'lid':lent[0],
'rid': rent[0],
'ltype': lent[1],
'rtype': rent[1],
'evidences': okEvs
})
"""
if entType.upper() == 'GENE':
for ev in rel['evidences']:
docid = ev.get('docid', None)
if docid != None:
seenPMIDs.add(docid)
data_source = ev.get('data_source', None)
seenEvidenceTypes[data_source] += 1
if rel['ltype'].upper() == entType.upper():
seenInteractors[rel['rtype']].add(rel['rid'])
else:
seenInteractors[rel['ltype']].add(rel['lid'])
seenMirnaIDs = set()
if entType.upper() == 'GENE':
for x in seenInteractors['mirna']:
txtMirna = x
try:
mirnaID = miRNA(txtMirna)
mirID = mirnaID.getPart(miRNAPART.ID, None)
mirID = int(mirID)
seenMirnaIDs.add(mirID)
except:
seenMirnaIDs.add(x)
answer = {
'search': genes,
'interactor_count': len(seenInteractors),
'interactor_types': [x for x in seenInteractors],
'data_source_count': len(seenEvidenceTypes),
'data_sources': [x for x in seenEvidenceTypes],
'evidence_count':
sum([seenEvidenceTypes[x] for x in seenEvidenceTypes]),
'interactors': list(seenMirnaIDs)
}
return app.make_response((jsonify(answer), 200, None))
entText = entity.attrib['text']
entType = entity.attrib['type']
entOffset = tuple(
[int(x) for x in entity.attrib['charOffset'].split("-")])
if entType in ["Specific_miRNAs", "Genes/Proteins"]:
if "Genes" in entType:
if entText in normGeneSymbols:
entText = normGeneSymbols[entText]
elif entText.upper() in normGeneSymbols:
gene = normGeneSymbols[entText.upper()]
else:
try:
entText = miRNA(entText).getStringFromParts([
miRNAPART.MATURE, miRNAPART.ID,
miRNAPART.PRECURSOR
])
except:
pass
entTuple = (entText, entType, (entOffset[0],
entOffset[1] + 1))
entId2elem[entId] = entTuple
sentEntText = sentText[entTuple[2][0]:entTuple[2][1]]
for pair in allPairs:
validInteraction = pair.attrib['interaction'].lower() == "true"
pairE1 = pair.attrib['e1']
pairE2 = pair.attrib['e2']
def getCoExpression():
global geneNeighbourHoods
global symbol2ensemblDB
global mi2mirna
interactReq = request.get_json(force=True, silent=True)
if interactReq == None:
return app.make_response((jsonify({'error':
'invalid json'}), 400, None))
allGenes = interactReq['genes']
if allGenes == None or len(allGenes) == 0:
return app.make_response((jsonify({'error': 'no genes'}), 400, None))
netw = ExpressionNetwork()
org2networg = {'mmu': "Mouse", 'hsa': "Human"}
genesByOrg = defaultdict(set)
for gene in allGenes:
ensGenes = symbol2ensemblDB.get_all_genes(gene)
if ensGenes == None or len(ensGenes) == 0:
ensGenes = {}
if gene.startswith("LNC"):
if "mm10" in gene:
ensGenes['mmu'] = {gene}
elif "hg38" in gene:
ensGenes["hsa"] = {gene}
else:
try:
miobj = miRNA(gene)
minum = miobj.getPart(miRNAPART.ID, None)
if minum != None:
mmuMI = mi2mirna.mirnaNum2mi.get(("mmu", minum), None)
hsaMI = mi2mirna.mirnaNum2mi.get(("hsa", minum), None)
if mmuMI != None:
ensGenes['mmu'] = {mmuMI}
if hsaMI != None:
ensGenes['hsa'] = {hsaMI}
except:
pass
for org in ensGenes:
for ensGeneID in ensGenes[org]:
genesByOrg[org2networg[org]].add(ensGeneID)
print("Genes by org")
for x in genesByOrg:
print(x, genesByOrg[x])
allEdges = []
for org in genesByOrg:
ensGenes = genesByOrg[org]
edges = netw.getEdgesFeature(ensGenes, org)
for edge in edges:
src = edge['source']
tgt = edge['target']
newsrc = symbol2ensemblDB.get_symbol_for_ensembl(src)
if newsrc == None and src.startswith("MI"):
newsrc = mi2mirna.mi2mirna.get(src, None)
if newsrc != None:
edge['source'] = newsrc
newtgt = symbol2ensemblDB.get_symbol_for_ensembl(tgt)
if newtgt == None and tgt.startswith("MI"):
newtgt = mi2mirna.mi2mirna.get(tgt, None)
if newtgt != None:
edge['target'] = newtgt
allEdges.append(edge)
print(allEdges)
return app.make_response((jsonify(allEdges), 200, None))
requestData['mirna'] = [miRName]
requestData['sentences'] = "true"
#print(requestData)
json = DataBasePlotter.fetchSimple(requestData)
allDocEvidences = defaultdict(lambda: defaultdict(list))
for x in json["rels"]:
genestr = x["lid"]
mirnastr = x["rid"]
accMir = None
try:
origTarget = miRNA(miRName)
target = miRNA(mirnastr)
accMir = origTarget
if not origTarget.accept(target,
compLevel=miRNACOMPARISONLEVEL.MATUREID):
print("Not accepted:", target, " as ", origTarget)
pass
except:
#print("skipping", x)
continue
#print(x["lid"], x["rid"], simpleStr)
gene2mirna = defaultdict(set)
for mirelPMID in [mirelPMIDhsa, mirelPMIDmmu]:
for gene in mirelPMID.ltype2rel:
allMirRels = mirelPMID.ltype2rel[gene]
allNormedMirs = set()
for rel in allMirRels:
relMir = rel.rid
try:
testMirna = miRNA(relMir)
nMirna = testMirna.getStringFromParts(
[miRNAPART.MATURE, miRNAPART.ID, miRNAPART.PRECURSOR])
allNormedMirs.add(nMirna)
except:
print("error loading miRNA", relMir)
for x in allNormedMirs:
gene2mirna[gene].add(x)
with open("/mnt/c/ownCloud/data/mirpredict/mirexplore_rels.tsv",
'w') as outfile:
for gene in gene2mirna:
allmirs = gene2mirna[gene]
for mirna in allmirs:
