def annotate(self, input_data):
out = {}
chrom = input_data['chrom']
pos = input_data['pos']
out = {'ncrnaclass': [], 'ncrnaname': []}
bins = get_ucsc_bins(pos)
pos = str(pos)
for bin in bins:
query = 'select class, name from ncrna ' +\
'where binno=' + str(bin) + ' and ' +\
'chrom="' + chrom + '" and ' +\
'start<=' + pos + ' and end>=' + pos
self.cursor.execute(query)
results = self.cursor.fetchall()
if len(results) == 0:
continue
for result in results:
(ncrna_class, ncrna_name) = result
out['ncrnaclass'].append(ncrna_class)
out['ncrnaname'].append(ncrna_name)
out['ncrnaclass'] = ','.join(out['ncrnaclass'])
out['ncrnaname'] = ','.join(out['ncrnaname'])
return out
def annotate(self, input_data):
out = {}
chrom = input_data['chrom']
pos = input_data['pos']
out = {'nhlbi': [], 'pmid': [], 'phenotype': []}
bins = get_ucsc_bins(pos)
pos = str(pos)
for bin in bins:
query = 'select nhlbi, pmid, pvalue, phenotype ' +\
'from grasp ' +\
'where chrom="' + chrom +\
'" and binno=' + str(bin) +\
' and pos=' + pos +\
' order by pvalue desc;'
self.cursor.execute(query)
results = self.cursor.fetchall()
if len(results) == 0:
continue
for result in results:
(nhlbi, pmid, pvalue, phenotype) = result
out['nhlbi'].append(nhlbi)
out['pmid'].append(pmid)
pvalue = '{:.4f}'.format(pvalue)
out['phenotype'].append(phenotype + '(' + str(pvalue) + ')')
out['nhlbi'] = ','.join([str(v) for v in out['nhlbi']])
out['pmid'] = ','.join([str(v) for v in out['pmid']])
out['phenotype'] = ','.join([str(v) for v in out['phenotype']])
if out['phenotype'] == '':
out = None
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select score from {chrom} where bin={bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
return {'score': row[0]}
def annotate(self, input_data, secondary_data=None):
chrom = input_data["chrom"]
pos = input_data["pos"]
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select region, ensr from ensembl where chrom = "{chrom}" and bin = {bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
out = {'region': row[0], 'ensr': row[1]}
else:
out = None
return out
def annotate(self, input_data):
out = {}
chrom = input_data['chrom']
start = input_data['pos']
ref = input_data['ref_base']
alt = input_data['alt_base']
reflen = len(ref)
altlen = len(alt)
if reflen == 1 and altlen == 1:
end = start
elif reflen == 1 and altlen > 1:
end = start
elif altlen == 1 and reflen > 1:
end = start + reflen - 1
elif reflen > 1 and altlen > 1:
end = start + reflen - 1
out = {'repeatclass': [],
'repeatfamily': [],
'repeatname': []}
has_annotation = False
bins = get_ucsc_bins(start, end)
for bin in bins:
query = 'select class, family, name ' +\
'from repeat ' +\
'where binno=' + str(bin) + ' and ' +\
'chrom="' + chrom + '" and ' +\
'start<=' + str(end) + ' and end>=' + str(start)
self.cursor.execute(query)
results = self.cursor.fetchall()
if len(results) == 0:
continue
for result in results:
has_annotation = True
(repeat_class, repeat_family, repeat_name) = result
out['repeatclass'].append(repeat_class)
out['repeatfamily'].append(repeat_family)
out['repeatname'].append(repeat_name)
if has_annotation:
out['repeatclass'] = ','.join(out['repeatclass'])
out['repeatfamily'] = ','.join(out['repeatfamily'])
out['repeatname'] = ','.join(out['repeatname'])
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select transcript, id, name, derives_from from mirbase where chrom="{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
out = {
'transcript': row[0],
'id': row[1],
'name': row[2],
'derives_from': row[3]
}
else:
out = None
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select pct, syn_density, cpg, cov_score, resid, redid_pctile from ccr where chrom = "{chrom}" and bin = {bin} and beg <= {pos} and end >= {pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
out = {
'pct': row[0],
'syn_density': row[1],
'cpg': row[2],
'cov_score': row[3],
'resid': row[4],
'resid_pct': row[5]
}
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select feature_name, score, id, target_genes from gene where chrom="{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
out = {
'feature_name': row[0],
'score': row[1],
'ident': row[2],
'target_genes': row[3]
}
else:
out = None
return out
def annotate(self, input_data, secondary_data=None):
if not secondary_data or len(secondary_data['hg19']) == 0:
return
chrom = secondary_data['hg19'][0]['chrom']
pos = secondary_data['hg19'][0]['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
self.cursor.execute(
f'select s.cell, s.quality, s.antibody, s.dccAccession, s.factor from {chrom} as c join studies as s on c.study=s.id where c.bin=? and c.beg<=? and c.end>?',
[lowbin, pos, pos],
)
rows = self.cursor.fetchall()
if rows:
studies = sorted([list(v) for v in rows], key=lambda x: x[2])
factor = sorted(list(set(map(lambda x: x[4], rows))),
key=str.lower)
return {
'factor': factor,
'all': studies,
}
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select acc_d, acc_e, _group, bound from screen where chrom = "{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
row = self.cursor.fetchone()
if row:
if row[3] == 'CTCF-bound':
bound = 'Yes'
else:
bound = None
return {
'acc_d': row[0],
'acc_e': row[1],
'_group': row[2],
'bound': bound
}
def annotate(self, input_data, secondary_data=None):
if not secondary_data or len(secondary_data['hg19']) == 0:
return
chrom = secondary_data['hg19'][0]['chrom']
pos = secondary_data['hg19'][0]['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
self.cursor.execute(
f'select s.cell, s.quality, s.antibody, s.dccAccession, s.factor from {chrom} as c join studies as s on c.study=s.id where c.bin=? and c.beg<=? and c.end>?',
[lowbin, pos, pos],
)
rows = self.cursor.fetchall()
if rows:
data = list(zip(*rows))
return {
'cell': ';'.join(data[0]),
'quality': ';'.join(data[1]),
'antibody': ';'.join(data[2]),
'study': ';'.join(data[3]),
'factor': ';'.join(data[4])
}
def annotate(self, input_data):
out = {}
chrom = input_data['chrom']
pos = input_data['pos']
out = {'pseudogene_hugo': [], 'pseudogene_transcript': []}
bins = get_ucsc_bins(pos)
pos = str(pos)
for bin in bins:
query = 'select tid ' +\
'from exon ' +\
'where chrom="' + chrom +\
'" and binno=' + str(bin) +\
' and start<=' + pos +\
' and end>=' + pos
self.cursor.execute(query)
results = self.cursor.fetchall()
if len(results) == 0:
continue
for result in results:
tid = str(result[0])
query = 'select enst, hugo from transcript where ' +\
'tid=' + tid
self.cursor.execute(query)
(enst, hugo) = self.cursor.fetchone()
out['pseudogene_hugo'].append(hugo)
out['pseudogene_transcript'].append(enst)
out['pseudogene_hugo'] = ','.join(out['pseudogene_hugo'])
out['pseudogene_transcript'] = ','.join(out['pseudogene_transcript'])
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select uniprotkb, desc, pubmed, filenames from binding where chrom = "{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom = chrom ,pos = pos, bin=lowbin)
self.cursor.execute(q)
rows = self.cursor.fetchall()
if rows is not None:
act_, binding_, ca_, dna_, metal_, np_, zn_, uniprots, pubmed = set(),set(), set(),set(),set(), set(),set(),set(), set()
all_results = []
out = {}
act, binding, ca, dna,metal,np,zn, pubmeds = '','','','','','','',''
for row in rows:
if row[3] == 'act':
act = row[1]
elif row[3] == 'biinding':
binding = row[1]
elif row[3] == 'ca':
ca = row[1]
elif row[3] == 'dna':
dna = row[1]
elif row[3] == 'metal':
metal = row[1]
elif row[3] == 'np':
np = row[1]
elif row[3] == 'zn':
zn = row[1]
new = str(row[2]).strip().split(';')
for i in range(len(new)):
pubmeds = new[i]
pubmeds = str(pubmeds).replace('None', '')
result = [row[0], act, binding, ca, dna, metal, np, zn, pubmeds]
all_results.append(result)
if pubmeds != '':
pubmed.add(pubmeds)
uniprots.add(row[0])
if act != '':
act_.add(act)
if binding != '':
binding_.add(binding)
if ca != '':
ca_.add(ca)
if dna != '':
dna_.add(dna)
if metal != '':
metal_.add(metal)
if np != '':
np_.add(np)
if zn != '':
zn_.add(zn)
pubmed = list(pubmed)
pubmed.sort()
uniprots = list(uniprots)
uniprots.sort()
act_ = list(act_)
act_.sort()
binding_ = list(binding_)
binding_.sort()
ca_ = list(ca_)
ca_.sort()
dna_ = list(dna_)
dna_.sort()
metal_ = list(metal_)
metal_.sort()
np_ = list(np_)
np_.sort()
zn_ = list(zn_)
zn_.sort()
if all_results:
out = {'uniprotkb': ';'.join(uniprots), 'act': ';'.join(act_), 'binding': ';'.join(binding_), 'ca': ';'.join(ca_), 'dna': ';'.join(dna_), 'metal': ';'.join(metal_), 'np': ';'.join(np_), 'zn': ';'.join(zn_),'pubmed': ';'.join(pubmed), 'all': all_results}
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select uniprotkb, desc, pubmed, filenames from protein where chrom = "{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom=chrom, pos=pos, bin=lowbin)
self.cursor.execute(q)
rows = self.cursor.fetchall()
if rows is not None:
domain, intramem, motif, peptide, repeat, topo, transmem, pubmeds = '', '', '', '', '', '', '', ''
domain_, intramem_, motif_, peptide_, repeat_, topo_, transmem_, uniprot_, pubmed_ = set(
), set(), set(), set(), set(), set(), set(), set(), set()
all_results = []
out = {}
for row in rows:
if row[3] == 'domain':
domain = row[1]
elif row[3] == 'intramem':
intramem = row[1]
elif row[3] == 'motif':
motif = row[1]
elif row[3] == 'peptide':
peptide = row[1]
elif row[3] == 'repeat':
repeat = row[1]
elif row[3] == 'topo':
topo = row[1]
elif row[3] == 'transmem':
transmem = row[1]
new = str(row[2]).strip().split(';')
for i in range(len(new)):
pubmeds = new[i]
result = [
row[0], domain, intramem, motif, peptide, repeat, topo,
transmem, pubmeds
]
all_results.append(result)
if pubmeds != '':
pubmed_.add(pubmeds)
uniprot_.add(row[0])
if domain != '':
domain_.add(domain)
if intramem != '':
intramem_.add(intramem)
if motif != '':
motif_.add(motif)
if peptide != '':
peptide_.add(peptide)
if repeat != '':
repeat_.add(repeat)
if topo != '':
topo_.add(topo)
if transmem != '':
transmem_.add(transmem)
pubmed_ = list(pubmed_)
pubmed_.sort()
uniprot_ = list(uniprot_)
uniprot_.sort()
domain_ = list(domain_)
domain_.sort()
intramem_ = list(intramem_)
intramem_.sort()
motif_ = list(motif_)
motif_.sort()
peptide_ = list(peptide_)
peptide_.sort()
repeat_ = list(repeat_)
repeat_.sort()
topo_ = list(topo_)
topo_.sort()
transmem_ = list(transmem_)
transmem_.sort()
if all_results:
out = {
'domain': ';'.join(domain_),
'intramem': ';'.join(intramem_),
'motif': ';'.join(motif_),
'peptide': ';'.join(peptide_),
'repeat': ';'.join(repeat_),
'topo': ';'.join(topo_),
'transmem': ';'.join(transmem_),
'uniprotkb': ';'.join(uniprot_),
'pubmed': ';'.join(pubmed_),
'all': all_results
}
return out
def annotate(self, input_data, secondary_data=None):
chrom = input_data['chrom']
pos = input_data['pos']
coding = input_data['coding']
so = input_data['so']
if chrom is None or pos is None:
return
lowbin = get_ucsc_bins(pos)[0]
q = 'select uniprotkb, desc, pubmed, filenames from ptm where chrom = "{chrom}" and bin={bin} and beg<={pos} and end>={pos}'.format(
chrom = chrom ,pos = pos, bin=lowbin)
self.cursor.execute(q)
rows = self.cursor.fetchall()
if rows is not None:
crosslnk_ ,disulfid_, carbohyd_, init_, lipid_, mod_, propep_, pubmed, signal_, transit_, uniprots = set(),set(),set(),set(),set(),set(),set(),set(),set(),set(),set()
crosslnk, disulfid, carbohyd, init,lipid,mod,propep, pubmeds,signal, transit = '','','','','','','','','',''
all_results = []
out = {}
for row in rows:
if coding != 'Y' and row[3] == 'propep' or coding != 'Y' and row[3] == 'signal' or coding != 'Y' and row[3] == 'transit':
continue
if row[3] == 'transit':
transit = row[1]
elif row[3] == 'mod':
mod = row[1]
elif row[3] == 'signal':
signal = row[1]
elif row[3] == 'propep':
propep = row[1]
elif row[3] == 'crosslnk':
crosslnk = row[1]
elif row[3] == 'carbohyd':
carbohyd = row[1]
elif row[3] == 'lipid':
lipid = row[1]
elif row[3] == 'init':
init = row[1]
elif row[3] == 'disulfid':
disulfid = row[1]
pub = str(row[2]).replace(',', ';')
new = pub.strip().split(';')
for i in range(len(new)):
pubmeds = new[i]
pubmeds = str(pubmeds).replace('None', '')
result = [row[0], crosslnk, carbohyd, init,lipid, mod,propep, signal, transit,disulfid, pubmeds]
all_results.append(result)
if pubmeds != '':
pubmed.add(pubmeds)
uniprots.add(row[0])
if transit != '':
transit_.add(transit)
if mod != '':
mod_.add(mod)
if signal != '':
signal_.add(signal)
if propep != '':
propep_.add(propep)
if crosslnk != '':
crosslnk_.add(crosslnk)
if carbohyd != '':
carbohyd_.add(carbohyd)
if lipid != '':
lipid_.add(lipid)
if init != '':
init_.add(init)
if disulfid != '':
disulfid_.add(disulfid)
mod_ = list(mod_)
mod_.sort()
signal_ = list(signal_)
signal_.sort()
propep_ = list(propep_)
propep_.sort()
crosslnk_ = list(crosslnk_)
crosslnk_.sort()
carbohyd_ = list(carbohyd_)
carbohyd_.sort()
lipid_ = list(lipid_)
lipid_.sort()
init_ = list(init_)
init_.sort()
disulfid_ = list(disulfid_)
disulfid_.sort()
transit_ = list(transit_)
transit_.sort()
uniprots = list(uniprots)
uniprots.sort()
pubmed = list(pubmed)
pubmed.sort()
if all_results:
out = {'disulfid': ';'.join(disulfid_), 'transit': ';'.join(transit_), 'mod': ';'.join(mod_), 'signal': ';'.join(signal_), 'propep': ';'.join(propep_), 'crosslnk': ';'.join(crosslnk_), 'carbohyd': ';'.join(carbohyd_), 'lipid': ';'.join(lipid_), 'init': ';'.join(init_),'uniprotkb': ';'.join(uniprots), 'pubmed': ';'.join(pubmed), 'all': all_results}
return out