pystream-protobuf 1.4.3

Python implementation of stream library

pyStream

Python implementation of stream library. Multiple protobuf messages can be written/read into/from a stream by using this library. It enables stream processing of protobuf messages and can be used for parsing all files encoded by stream library and writing protobuf instances into a file by the same encoding. Refer to the library github page for more information about formatting.

Installation

You can install pyStream using pip:

pip install pystream-protobuf

Examples

Here’s a sample code using the Stream class to read a file (so-called GAM file) containing a set of VG’s Alignment objects (defined here). It yields the protobuf objects stored in the file:

import stream
import vg_pb2

alns = [a for a in stream.parse('test.gam', vg_pb2.Alignment)]

Or use lower-level method open in order to have more control in opening the stream and reading data:

import stream
import vg_pb2

alns_list = []
with stream.open('test.gam', 'rb') as istream:
    for data in istream:
        aln = vg_pb2.Alignment()
        aln.ParseFromString(data)
        alns_list.append(aln)

This example also does the same without using with statement by calling close method explicitly after reading the data:

import stream
import vg_pb2

alns_list = []
istream = stream.open('test.gam', 'rb')
for data in istream:
    aln = vg_pb2.Alignment()
    aln.ParseFromString(data)
    alns_list.append(aln)
istream.close()

And here is another sample code for writing multiple protobuf objects into a file (here a GAM file):

import stream

stream.dump('test.gam', *objects_list, buffer_size=10)

Or using open method for lower-level control – here, appending for example:

import stream

with stream.open('test.gam', 'ab') as ostream:
    ostream.write(*objects_list)
    ostream.write(*another_objects_list)

Or without using with statement where the data is written after calling close method explicitly:

import stream

ostream = stream.open('test.gam', 'wb')
ostream.write(*objects_list)
ostream.write(*another_objects_list)
ostream.close()

More features

Buffered write

By default, all protobuf message objects provided on each call are written in a group of messages. The messages can be buffered and write to the stream in a group of fixed size whenever possible. The size of the buffer can be changed (from default value 0 — no buffer) by passing it through keyword argumnet buffer_size when Stream class is constructed or a stream is opened. This value is the number of objects which should be written in a group.

Grouping message

Messages can be grouped in varied size when writing to a stream by setting buffer size sufficiently large or infinity (-1) and calling flush method of Stream class whenever desired.

Group delimiter

Group of objects can be separated by a delimiter of the choice (or by default None) when reading from a stream. Sometimes, it can help to identify the end of a group which is hidden from the library user by default. This feature can be enable by setting group_delimiter True when constructing a Stream instance or openning a stream. The delimiter class can also be specified by delimiter_cls.