def getNumOfDonorsWithBuckets(symb):
df = pd.read_csv('../merged_1.6.1.csv')
try:
symbolResponse = json.load(
urllib.request.urlopen(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"
))
chromosome = int(symbolResponse['seq_region_name'])
if symbolResponse['assembly_name'] == 'GRCh37':
start = plotBuilder.lift(symbolResponse['start'], chromosome)
end = plotBuilder.lift(symbolResponse['end'], chromosome)
else:
start = symbolResponse['start']
end = symbolResponse['end']
except Exception as e:
print(e)
print(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"
)
print(f"symb got fricked")
return
df = df[(((df['seqnames'] == chromosome) &
(df['start'].between(start, end, inclusive=True))) |
((df['altchr'] == chromosome) &
(df['altpos'].between(start, end, inclusive=True))))]
# more options can be specified also
return df['donor_unique_id'].value_counts().tolist()
def getNumOfSVsPerDonor(symb):
df = pd.read_csv('../merged_1.6.1.csv')
try:
symbolResponse = json.load(
urllib.request.urlopen(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"
))
chromosome = int(symbolResponse['seq_region_name'])
if symbolResponse['assembly_name'] == 'GRCh37':
start = plotBuilder.lift(symbolResponse['start'], chromosome)
end = plotBuilder.lift(symbolResponse['end'], chromosome)
else:
start = symbolResponse['start']
end = symbolResponse['end']
except Exception as e:
print(e)
print(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"
)
print(f"symb got fricked")
return
df = df[(((df['seqnames'] == chromosome) &
(df['start'].between(start, end, inclusive=True))) |
((df['altchr'] == chromosome) &
(df['altpos'].between(start, end, inclusive=True))))]
unique_ids = df['donor_unique_id'].unique()
forPlot = []
for uniID in unique_ids:
place = df[(df['donor_unique_id'] == uniID)]
forPlot.append(len(place.index))
return forPlot
def getSNVsPerPatient(symb):
df = pd.read_csv('../merged_1.6.1.csv')
try:
patients = df['donor_unique_id'].unique()
for patient in patients:
patientResponse = json.load(urllib.request.urlopen(
f"https://dcc.icgc.org/api/v1/keywords?q=CPCG0128&filters=%7B%7D&from=1&size=10"))
symbolResponse = json.load(urllib.request.urlopen(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"))
chromosome = int(symbolResponse['seq_region_name'])
if symbolResponse['assembly_name'] == 'GRCh37':
start = plotBuilder.lift(symbolResponse['start'], chromosome)
end = plotBuilder.lift(symbolResponse['end'], chromosome)
else:
start = symbolResponse['start']
end = symbolResponse['end']
except Exception as e:
print(e)
print(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1")
print(f"symb got fricked")
return
df = df[(((df['seqnames'] == chromosome) & (df['start'].between(start, end, inclusive=True))) |
((df['altchr'] == chromosome) & (df['altpos'].between(start, end, inclusive=True))))]
# more options can be specified also
unique_ids = df['donor_unique_id'].unique()
forPlot = []
return (len(df.index))
def getStartAndEnd(symb):
try:
symbolResponse = json.load(urllib.request.urlopen(
f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symb}?content-type=application/json;expand=1"))
chromosome = int(symbolResponse['seq_region_name'])
if symbolResponse['assembly_name'] == 'GRCh37':
start = plotBuilder.lift(symbolResponse['start'], chromosome)
end = plotBuilder.lift(symbolResponse['end'], chromosome)
else:
start = symbolResponse['start']
end = symbolResponse['end']
return [chromosome, range(start, end)]
except:
print(symb)
return None