def fetch_generator(tabix, contig):
fetch = tabix.fetch(contig)
rows = map(lambda x: x.split('\t'), fetch)
annos = (row for row in rows if "CodingTranscript" in row[9])
json_rows = map(_map_line_to_json, annos)
json_rows = (row for row in json_rows if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "cadd") for rg in row_groups)
def fetch_generator(tabix, contig):
fetch = tabix.fetch(contig)
rows = map(lambda x: x.split('\t'), fetch)
annos = (row for row in rows if "CodingTranscript" in row[9])
json_rows = map(_map_line_to_json, annos)
json_rows = (row for row in json_rows if row)
row_groups = (it
for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "cadd") for rg in row_groups)
def load_data(input_file):
open_file = open("%s.tsv" % input_file)
open_file = csv.reader(open_file, delimiter="\t")
open_file.next()
grasp = imap(row_generator, open_file)
grasp = ifilter(lambda row: row[58] != "", grasp)
json_rows = imap(_map_line_to_json, grasp)
json_rows = (row for row in json_rows if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "grasp") for rg in row_groups)
def load_data(input_file):
open_file = open('%s.tsv' % input_file)
open_file = csv.reader(open_file, delimiter="\t")
open_file.next()
grasp = map(row_generator, open_file)
grasp = ifilter(lambda row: row[58] != "", grasp)
json_rows = map(_map_line_to_json, grasp)
json_rows = (row for row in json_rows if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "grasp") for rg in row_groups)
def load_data(input_file):
"""
write_file output and csv.reader input_file
'/opt/myvariant.info/load_archive/drugbank/drugbank.csv'
"""
open_file = open(input_file)
drugbank = csv.reader(open_file, delimiter=',')
drugbank.next()
json_rows = imap(_map_line_to_json, drugbank)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row['_id']))
return (merge_duplicate_rows(rg, 'drugbank') for rg in row_groups)
def data_generator(input_file):
# sort by the first column (hgvs id returned from Mutalyzer)
os.system("sort -k1 -n %s > %s.sorted" % (input_file, input_file))
open_file = open("%s.sorted" % (input_file))
emv = csv.reader(open_file, delimiter=",")
# Skip header
emv.next()
emv = filter(lambda x: x[0], emv)
json_rows = map(_map_line_to_json, emv)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "emv") for rg in row_groups)
def data_generator(input_file):
open_file = open(input_file)
evs = csv.reader(open_file, delimiter=" ")
# Skip first 8 meta lines
evs = islice(evs, 8, None)
evs = (row for row in evs if ":" in row[30] and
len(row) == VALID_COLUMN_NO)
# skip rows with multiple mutations
evs = (row for row in evs if len(row[3].split(";")) == 1)
json_rows = map(_map_line_to_json, evs)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "evs") for rg in row_groups)
def data_generator(input_file, version):
open_file = open(input_file)
evs = csv.reader(open_file, delimiter=" ")
# Skip first 8 meta lines
evs = islice(evs, 8, None)
evs = (row for row in evs
if ":" in row[30] and len(row) == VALID_COLUMN_NO)
# skip rows with multiple mutations
evs = (row for row in evs if len(row[3].split(";")) == 1)
json_rows = map(_map_line_to_json, version=version, evs)
row_groups = (it
for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "evs") for rg in row_groups)
def load_data(input_file):
os.system("sort -t$'\t' -k14 -k15 -k20 -n %s > %s_sorted.tsv" \
% (input_file, input_file))
open_file = open("%s_sorted.tsv" % (input_file))
print input_file
clinvar = csv.reader(open_file, delimiter="\t")
clinvar = (row for row in clinvar
if row[18] != '-' and row[18].find('?') == -1 and row[13] != ""
and row[12] == "GRCh37" and not re.search(r'p.', row[18]))
json_rows = (row for row in imap(_map_line_to_json, clinvar) if row)
row_groups = (it
for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "clinvar") for rg in row_groups)
def fetch_generator(tabix, contig):
dbfile_path = 'home/kevinxin/cadd/' + 'cadd_id' + contig
db = dbm.open(dbfile_path)
ids = db.keys()
set_ids = set(ids)
print(len(ids))
fetch = tabix.fetch(contig)
rows = imap(lambda x: x.split('\t'), fetch)
# looking for annotype as 'codingtranscript', 'noncodingtranscript'
annos = (row for row in rows if "CodingTranscript" in row[9] or
get_hgvs_from_vcf(row[0], row[1], row[2], row[4]) in set_ids)
json_rows = imap(_map_line_to_json, annos)
json_rows = (row for row in json_rows if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "cadd") for rg in row_groups)
def load_data(input_file):
os.system("sort -t$'\t' -k14 -k15 -k20 -n %s > %s_sorted.tsv" \
% (input_file, input_file))
open_file = open("%s_sorted.tsv" % (input_file))
print input_file
clinvar = csv.reader(open_file, delimiter="\t")
clinvar = (row for row in clinvar
if row[18] != '-' and
row[18].find('?') == -1 and
row[13] != "" and
row[12] == "GRCh37" and
not re.search(r'p.', row[18]))
json_rows = (row for row in imap(_map_line_to_json, clinvar) if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row:
row["_id"]))
return (merge_duplicate_rows(rg, "clinvar") for rg in row_groups)
def fetch_generator(tabix, contig):
dbfile_path = 'home/kevinxin/cadd/' + 'cadd_id' + contig
db = dbm.open(dbfile_path)
ids = db.keys()
set_ids = set(ids)
print(len(ids))
fetch = tabix.fetch(contig)
rows = imap(lambda x: x.split('\t'), fetch)
# looking for annotype as 'codingtranscript', 'noncodingtranscript'
annos = (row for row in rows if "CodingTranscript" in row[9]
or get_hgvs_from_vcf(row[0], row[1], row[2], row[4]) in set_ids)
json_rows = imap(_map_line_to_json, annos)
json_rows = (row for row in json_rows if row)
row_groups = (it
for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "cadd") for rg in row_groups)
def load_data(input_file):
# os.system("sort -t$'\t' -k18 -k14 %s > %s_sorted.tsv" % (input_file, input_file))
# open_file = open("%s_sorted.tsv" % (input_file))
open_file = open(input_file)
open_file = csv.reader(open_file, delimiter="\t")
cosmic = []
for row in open_file:
try:
c = row[13].split(".")[1]
except:
c = ""
row.append(row[17].split("-")[0] + "." + c)
cosmic.append(row)
if row[-1] != "":
print row[-1]
cosmic = sorted(cosmic, key=operator.itemgetter(17), reverse=True)
cosmic = ifilter(lambda row:
row[17] != "" and
row[13] != "", cosmic)
json_rows = imap(_map_line_to_json, cosmic)
json_rows = (row for row in json_rows if row)
row_groups = (it for (key, it) in groupby(json_rows, lambda row: row["_id"]))
return (merge_duplicate_rows(rg, "cosmic") for rg in row_groups)