pystream-protobuf 1.1

Python implementation of stream library

Python implementation of stream library for parsing all files encoded by stream and writing protobuf instances into the file by using the same encoding.

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()