semvec/pypi-packages huggingface dataset:
genomediff 0.4.1
GenomeDiff (*.gd) file reader
License: MIT
Requires Python: >=3.0

genomediff-python
=================

**genomediff-python** parses files in the
`GenomeDiff format <http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_format.html>`_
generated by the `breseq <http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html>`_
variant caller for haploid microbial organisms.


Installation
------------

::

    python setup.py install


Only Python 3.x is tested.

Usage
-----

GenomeDiff files are read using ``GenomeDiff.read(file)``. The ``GenomeDiff`` object contains a ``metadata`` dict with
the metadata, as well as ``mutations``, ``evidence`` and ``validation`` lists—each containing records of that type.
Records can be accessed through this list or by id. ``GenomeDiff`` is iterable and iterating will return all records of all types.

::

    >>> from genomediff import *
    >>> document = GenomeDiff.read(open('MyDiff.gd', 'r', encoding='utf-8'))
    >>> document.metadata
    {'GENOME_DIFF': '1.0', 'AUTHOR': ''}
    >>> document.mutations[0]
    Record('SNP', 1, [191], new_seq='A', seq_id='NC_000913', snp_type='intergenic',  position=12346)
    >>> document.mutations[0].parent_ids
    [191]
    >>> document[191]
    Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)
    >>> document.mutations[0].parents
    [Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)]
    >>> document.write(open('NewDiff.gd', 'w', encoding='utf-8'))
py-assembly-payments 1.0.0
Python wrapper around the Assembly Payments API
License: MIT

# py-assembly-payments
Unofficial Python client for the Assembly Payments API

## 🚧 In Development 🚧
This package is still undergoing development and is pre-v1. It currently implements around 30% of the Assembly Payments API. You can keep up with the [coverage here](https://github.com/divipayhq/py-assembly-payments/projects/1)

## Installation
```
pip install py-assembly-payments
```

## Example
```python
from assembly_payments.client import AssemblyClient

client = AssemblyClient(client_id=CLIENT_ID, client_secret=CLIENT_SECRET)

# List Users
client.users.list()

# Create User
user = client.users.create(
    id="your-user-id",
    first_name="Jane",
    last_name="Doe",
    email="jane.doe@example.com"
)

# Easy object access
print(user.first_name + user.last_name) # Jane Doe
```

## Credentials
You can set your auth credentials in two ways:

1. Through arguments to the client:
```python
AssemblyClient(client_id=CLIENT_ID, client_secret=CLIENT_SECRET, scope=CLIENT_SCOPE, grant_type="client_credentials")
```

2. Through environment variable which `AssemblyClient` will pick up from:

```bash
export ASSEMBLY_CLIENT_ID=my-client-id
export ASSEMBLY_CLIENT_SECRET=my-client-secret
export ASSEMBLY_SCOPE=my-scope
```

`grant_type` defaults to `"client_credentials"` and can only be controlled by an argument to `AssemblyClient`.