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filename += '.csv' if args.csv else '.tsv'
if not args.overwrite and os.path.exists(filename):
parser.exit(1, fill('Error: path \"' + filename + '\" already exists but -f/--overwrite was not set') + '\n')
writer = csv.writer(open(filename, 'wb'),
delimiter=delimiter)
if not args.no_header:
writer.writerow((['__id__:int'] if args.rowid else []) + [(col['name'] + ':' + col['type']) for col in dxtable.describe()['columns']])
# Query stuff
if args.gri is not None:
try:
lo = int(args.gri[1])
hi = int(args.gri[2])
except:
parser.exit(1, fill('Error: the LO and HI arguments to --gri must be integers') + '\n')
gri_query = dxpy.DXGTable.genomic_range_query(args.gri[0],
lo,
hi,
args.gri_mode,
args.gri_name)
iterator = dxtable.iterate_query_rows(query=gri_query, limit=args.limit)
else:
iterator = dxtable.iterate_rows(start=args.starting, end=(None if args.limit is None else args.starting + args.limit))
for row in iterator:
writer.writerow([str(item).encode('utf-8') for item in row[0 if args.rowid else 1:]])
if opts.genes_id == None:
parser.print_help()
sys.exit(1)
if opts.file_name != None:
outputFile = open(opts.file_name, 'w')
else:
outputFile = None
if opts.genes_id == None:
parser.print_help()
sys.exit(1)
tableId = opts.genes_id
table = dxpy.DXGTable(tableId)
genesTypes = {"exon": True, "CDS":True, "5' UTR": True, "3' UTR": True, "transcript":True, "gene":True}
translatedTypes = {"transcript":"mRNA", "5' UTR": "five_prime_UTR", "3' UTR":"three_prime_UTR"}
columns = table.get_col_names()
idColumn = None
parentColumn = None
if "ID" in columns:
idColumn = "ID"
elif "Id" in columns:
idColumn = "Id"
elif "id" in columns:
idColumn = "id"
else:
idColumn = "span_id"
def main(**kwargs):
if len(kwargs) == 0:
kwargs = vars(arg_parser.parse_args(sys.argv[1:]))
if "end_row" not in kwargs:
kwargs["end_row"] = None
if kwargs["end_row"] is not None and kwargs["end_row"] <= kwargs["start_row"]:
arg_parser.error("End row %d must be greater than start row %d" % (kwargs["end_row"], kwargs["start_row"]))
try:
table = dxpy.DXGTable(kwargs['reads_table'])
except:
raise dxpy.AppError("Failed to open table for export")
existCols = table.get_col_names()
### sort out columns to download
col = []
col2 = []
# if there's a second sequence, it's paired
if "sequence2" in existCols:
isPaired = True
else:
isPaired = False
{"name": "type", "type": "string"},
{"name": "strand", "type": "string"},
{"name": "score", "type": "float"},
{"name": "is_coding", "type": "boolean"},
{"name": "parent_id", "type": "int32"},
{"name": "frame", "type": "int16"},
{"name": "description", "type": "string"},
{"name": "source", "type": "string"}]
additionalColumns = []
for k, v in attributes.iteritems():
if k not in reservedColumns and len(k) < 100:
schema.append({"name": k, "type": "string"})
additionalColumns.append(k)
indices = [dxpy.DXGTable.genomic_range_index("chr","lo","hi", 'gri'),
dxpy.DXGTable.lexicographic_index([
dxpy.DXGTable.lexicographic_index_column("name", True, False),
dxpy.DXGTable.lexicographic_index_column("chr"),
dxpy.DXGTable.lexicographic_index_column("lo"),
dxpy.DXGTable.lexicographic_index_column("hi"),
dxpy.DXGTable.lexicographic_index_column("type")], "search")]
spansTable = dxpy.new_dxgtable(columns=schema, indices=indices)
return spansTable, additionalColumns
("lo", "int32"),
("hi", "int32"),
("name", "string"),
("span_id", "int32"),
("type", "string"),
("strand", "string"),
("is_coding", "boolean"),
("parent_id", "int32"),
("frame", "int16"),
("description", "string")]
column_descs = [dxpy.DXGTable.make_column_desc(name, type) for name, type in columns]
indices = [dxpy.DXGTable.genomic_range_index("chr","lo","hi", 'gri'),
dxpy.DXGTable.lexicographic_index([
dxpy.DXGTable.lexicographic_index_column("name", True, False),
dxpy.DXGTable.lexicographic_index_column("chr"),
dxpy.DXGTable.lexicographic_index_column("lo"),
dxpy.DXGTable.lexicographic_index_column("hi"),
dxpy.DXGTable.lexicographic_index_column("type")], "search")]
default_row = ["", 0, 0, "", -1, "", ".", False, -1, -1, ""]
with open(bed_file, 'rU') as bed, dxpy.new_dxgtable(column_descs, indices=indices, mode='w') as span:
span_table_id = span.get_id()
details = {"original_contigset": dxpy.dxlink(ref_id)}
if file_id != None:
details["original_file"] = dxpy.dxlink(file_id)
if len(property_keys) != len(property_values):
raise dxpy.AppError("Expected each provided property to have a corresponding value.")
for i in range(len(property_keys)):