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Project Description

pyStream

Python implementation of stream library. Multiple protobuf messages can be written into 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_list = []
with stream.open("test.gam", "rb") as istream:
    for data in istream:
        aln = vg_pb2.Alignment()
        aln.ParseFromString(data)
        alns_list.append(aln)

Or

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

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

Or

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.

Release History

Release History

1.3.4

This version

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1.2.2

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1.2.1

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1.2.0rc0

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1.1.4

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1.1.3

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1.1.2

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1.1.1

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1.1

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1.0

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0.9.2

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0.9.1

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0.9

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Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pystream-protobuf-1.3.4.tar.gz (6.5 kB) Copy SHA256 Checksum SHA256 Source Nov 7, 2016

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