https://github.com/nanoporetech/bripy

Bam Read Index for python
https://github.com/nanoporetech/bripy

Last synced: about 1 year ago
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Bam Read Index for python

• Host: GitHub
• URL: https://github.com/nanoporetech/bripy
• Owner: nanoporetech
• License: other
• Created: 2019-12-07T10:18:26.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-12-07T10:20:37.000Z (over 6 years ago)
• Last Synced: 2025-04-06T08:02:14.507Z (over 1 year ago)
• Language: C
• Size: 140 KB
• Stars: 4
• Watchers: 17
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

          


![Oxford Nanopore Technologies logo](https://github.com/nanoporetech/bripy/raw/master/images/ONT_logo_590x106.png)

Bripy

======

Bripy is a python library for extracting reads from a bam by read name. It

uses the [bri](https://github.com/jts/bri) library from Jared Simpson.

© 2019 Oxford Nanopore Technologies Ltd.

Installation

------------

`bripy` can be installed using pip:

    pip install bripy

For python3.5 and python3.6 under linux this will download precompiled

binaries, in other environments a source distribution will be downloaded

and compiled. Compilation from source requires the same libraries as

[htslib](https://github.com/samtools/htslib):

    'm', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'

since htslib is built from source as part of the process.

Usage

-----

The library contains a single class interface and two example programs. To

index a bam file for later retrieval of reads run:

    bripy index 

This program is analogous to the `bri index  

Again this program is analogous to running `bri get  `.

The `bripy` API is simple, the following will return a string containing

sam formatted alignments:

    bri = BamReadIndex(bam_file)

    sam_data = bri.get_alignments(read_name)

This API is likely to change in future to provide a more useful data structure

akin to a `pysam.AlignedSegment`.

License

-------

**Licence and Copyright**

© 2019 Oxford Nanopore Technologies Ltd.

`bripy` is distributed under the terms of the Mozilla Public License 2.0.

**Research Release**

Research releases are provided as technology demonstrators to provide early

access to features or stimulate Community development of tools. Support for

this software will be minimal and is only provided directly by the developers.

Feature requests, improvements, and discussions are welcome and can be

implemented by forking and pull requests. However much as we would

like to rectify every issue and piece of feedback users may have, the

developers may have limited resource for support of this software. Research

releases may be unstable and subject to rapid iteration by Oxford Nanopore

Technologies.