semvec/pypi-packages huggingface dataset:
streaming-pileupy 0.5.7
Create multi-sample text-pileups of streaming SAM/BAM files.
License: MIT license
Requires Python: >=3.6
Keywords: streaming_pileupy

=================
Streaming Pileupy
=================


.. image:: https://img.shields.io/pypi/v/streaming_pileupy.svg
        :target: https://pypi.python.org/pypi/streaming_pileupy

.. image:: https://img.shields.io/travis/winni2k/streaming_pileupy.svg
        :target: https://travis-ci.com/winni2k/streaming_pileupy

.. image:: https://readthedocs.org/projects/streaming-pileupy/badge/?version=latest
        :target: https://streaming-pileupy.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status


.. image:: https://pyup.io/repos/github/winni2k/streaming_pileupy/shield.svg
     :target: https://pyup.io/repos/github/winni2k/streaming_pileupy/
     :alt: Updates



Create multi-sample text-pileups of streaming SAM/BAM files.


* Free software: MIT license
* Documentation: https://streaming-pileupy.readthedocs.io.


Features
--------

Streaming Pileupy creates a pileup of a single SAM/BAM file
using the read group SM identifier to split reads by sample:

.. code-block:: bash

    # extract sample names from read group SM tag
    samtools view -H input.bam \
      | grep '^@RG' \
      | perl -pne 's/.*SM:(\S+).*/$1/' \
      | sort | uniq > sample_names.txt

    # create read-group aware pileup
    spileup input.bam sample_names.txt

Base quality filtering
``````````````````````

Bases with less than a certain quality can be filtered with ``-Q``.


Missing features
----------------

* Read beginning and end annotations in pileup output
* Deletion annotations in pileup output
* Filter output bases on BED file

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.5.0 (2020-05-05)
------------------

* Add base quality filter (-Q)

0.4.0 (2020-05-05)
------------------

* Add support for python 3.6

0.3.0 (2020-05-05)
------------------

* Add support for basic pileup functionality

0.2.1 (2020-05-04)
------------------

* First release on PyPI.
github-releaser 0.2.1
CLI for creating releases on GitHub.
License: MIT license
Requires Python: >=3.5
Keywords: github-releaser

# github-releaser

`github-releaser` is a command-line tool for creating releases on GitHub.

## Installation

`pipenv install github-releaser`

## Usage

### Creating a release

To create a release, use the command `create-release`, e.g.:
```shell script
github-releaser create-release --account myuser --repository myrepo --tag-name v1.0.10
```

The example above will create a new release with a name and tag set to `v1.0.10` at `myuser/myrepo`. The option 
`--release-name` is optional, and if not specified the release name will be the same as the value of the `--tag-name`, in 
this case: `v1.0.10`

To see all the options use: `github-releaser create-release --help`

### Uploading assets

The command `upload-assets` to add assets to a release. Note that to upload assets a release must have been previously
created.

Give that there is already a release `v1.0.10` at `myuser/myrepo`, it is possible to add assets with the following command:
```shell script
github-releaser upload-assets --account myuser --repository myrepo --tagname v1.0.10 assets/*.zip
```

The example above uploads all `.zip` files from the `assets` directory to a release `v1.0.10` at `myuser/myrepo`.

To see all the options use: `github-releaser upload-assets --help`

### Commit and push files to a branch

Sometimes it is useful to commit and push new files to a specific branch. One possible scenario is
when files are auto-generated during a build in a CI environment, and there is a requirement to
include them to a branch. For example:

```shell script
github-releaser push-files --account myuser --repository myrepo myfile.txt
```
In this example, a file named `myfile.txt` is added to the `master` at `myuser/myrepo`

To see all the options use: `github-releaser push-files --help`


### GitHub's personal access token

It is required to use a GitHub's personal access token to use the commands described above.
The personal access token can be passed directly in the command line using the option `--token` or
set to an environment variable called `GITHUB_TOKEN`.
More information on how to create a GitHub's token can
be found [here](https://docs.github.com/en/github/authenticating-to-github/creating-a-personal-access-token)

## Copyright and License

Copyright (c) 2020 Daniel Furtado. Code released under MIT license

## Credits

This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.


# History

### 0.1.0 (2020-05-30)

* First release on PyPI.

### 0.1.1 (2020-06-02)

* Renamed the environment variable to `GITHUB_TOKEN`
* Updated documentation on how to pass token to `github-releaser` and
information on how to create the token on GitHub.

### 0.2.0 (2020-07-09)
* Include command `push-files`
* Updated documentation
* Minor code cleanup

### 0.2.1 (2020-08-04)
* Renamed push-file's command flag from `--msg` to `--m`
* Minor fixes