dbgz 0.5.0

Python library to load DBGZ files

dbgz

DBGZ (Data block "GNU" zip) is a lightweight seekable compressed binary format for storing and retrieving data. The format is designed to hold schema and data comprising primary objects, such as numbers, strings and arrays, as well as more complicated instances via msgpack, such as dictionaries and python objects. It is based on the bgzip file format used in biology and other fields.

This utility can be used to write and read DBGZ files in python.

Installation

Install using pip

pip install dbgz

or from source:

pip git+https://github.com/filipinascimento/dbgz.git

Usage

First import dbgz:

import dbgz

Defining a scheme

scheme = [
    ("anInteger","i"),
    ("aFloat","f"),
    ("aString","s"),
    ("anIntArray","I"),
    ("aFloatArray","F"),
    ("anStringArray","S"),
    ("anyType","a"), #any data type
]

Writing some data to a dbgz file

from tqdm.auto import tqdm # Optional, to print progress bar
# pip install tqdm

totalCount = 1000000;
with dbgz.DBGZWriter("test.dbgz",scheme) as fd:
    # New entries can be added as:
    fd.write(anInteger=1, aString="1")
    fd.write(anInteger=2, aString="2", aFloat=5)
    fd.write(anInteger=3, aString="3",anIntArray=list(range(10)), aFloatArray=[0.1,0.2,0.3,0.5])

    # Here is a loop to write a lot of data:
    for index in tqdm(range(totalCount)):
        fd.write(
            anInteger=index,
            aFloat=index*0.01,
            anIntArray=list(range(index,index+10)),
            aString=str(index),
            aFloatArray=[index+0.1,index-0.2,index+0.3,index+0.4],
            anStringArray=[str(index),str(index+1),str(index+2),str(index+3)],
            anyType={"a": index, "b": index+1, "c": index+2}
        )

Reading the dbgz file sequencially:

with dbgz.DBGZReader("test.dbgz") as fd:
    print(fd.scheme)
    for entry in tqdm(fd.entries,total=fd.entriesCount):
        assert entry["anInteger"] == int(entry["aString"])

Loading a dbgz file manually by using the read() method:

with dbgz.DBGZReader("test.dbgz") as fd:
    pbar = tqdm(total=fd.entriesCount)
    print(fd.scheme)
    while True:
        entries = fd.read(10)
        if(not entries):
            break
        for entry in entries:
            assert entry["anInteger"] == int(entry["aString"])
        pbar.update(len(entries))
pbar.refresh()
pbar.close()

Saving dictionary to file and loading it again

with dbgz.DBGZReader("test.dbgz") as fd:
    indexDictionary = fd.generateIndex("anInteger",
        indicesPath=None,
        filterFunction=lambda entry: entry["anInteger"]<10,
        useDictionary=True,
        showProgressbar = True
        )
    for key,values in indexDictionary.items():
        print(key,values)
        for value in values:
            assert int(key) == fd.readAt(value)[0]["anInteger"]

Saving dictionary to file and loading it again

with dbgz.DBGZReader("test.dbgz") as fd:
    fd.generateIndex(
        key = "anInteger",
        indicesPath="test_byAnInteger.idbgz", 
        filterFunction=lambda entry: entry["anInteger"]<10,
        useDictionary=True,
        showProgressbar = True
        )

    indexDictionary = dbgz.readIndicesDictionary("test_by.idbgz")
    for key,values in indexDictionary.items():
        print(key,values)
        for value in values:
            assert int(key) == fd.readAt(value)[0]["anInteger"]

Using a custom key generator for the index:

with dbgz.DBGZReader("test.dbgz") as fd:
    fd.generateIndex(
        keyFunction=lambda entry: entry["anyType"]["b"] if entry["anyType"] else None,
        indicesPath="test_byAnyType_b.idbgz", 
        filterFunction=lambda entry: entry["anInteger"]<10,
        useDictionary=True,
        showProgressbar = True
        )

    indexDictionary = dbgz.readIndicesDictionary("test_byAnyType_b.idbgz")
    for key,values in indexDictionary.items():
        print(key,values)
        for value in values:
            entry = fd.readAt(value)[0]
            assert int(key) == entry["anyType"]["b"] if entry["anyType"] else None