How to use the dxpy.DXGTable.lexicographic_index_column function in dxpy

To help you get started, we’ve selected a few dxpy examples, based on popular ways it is used in public projects.

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dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_gtf_to_genes.py View on Github

{"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) &lt; 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

dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_bed_to_spans.py View on Github

("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"])

dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_gff_to_genes.py View on Github

{"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) &lt; 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

dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_gtf_to_genes.py View on Github

{"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) &lt; 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

dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_gff_to_genes.py View on Github

{"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) &lt; 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

dnanexus / dx-toolkit / src / python / dxpy / scripts / dx_gff_to_genes.py View on Github

{"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) &lt; 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

How to use the dxpy.DXGTable.lexicographic_index_column function in dxpy

To help you get started, we’ve selected a few dxpy examples, based on popular ways it is used in public projects.

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