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{"name": "parent_id", "type": "int32"},
{"name": "frame", "type": "int16"},
{"name": "description", "type": "string"},
{"name": "source", "type": "string"},
{"name": "gene_id", "type": "string"},
{"name": "transcript_id", "type": "string"}]
additionalColumns = ['gene_id', 'transcript_id']
for k, v in attributes.iteritems():
if k != '' and k != 'gene_id' and k != 'transcript_id' 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
("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)):
details[property_keys[i]] = property_values[i]
span.set_details(details)
span.add_types(["gri", "Genes"])
{"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
{"name": "description", "type": "string"},
{"name": "source", "type": "string"},
{"name": "gene_id", "type": "string"},
{"name": "transcript_id", "type": "string"}]
additionalColumns = ['gene_id', 'transcript_id']
for k, v in attributes.iteritems():
if k != '' and k != 'gene_id' and k != 'transcript_id' 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
{"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
{"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