semvec/pypi-packages huggingface dataset:
damaged-reads-simulator 0.1.1
A simulator for damaged DNA reads with base quality recalibration
Requires Python: >=3.8
Keywords: bioinformatics, dna, sequencing, simulation, base-quality

# Damaged reads_simulator
Simulates NGS sequenced reads

## Installation
```
python3 -m venv readsim_env
source readsim_env/bin/activate

pip install damaged-reads-simulator
```
for prototyping with marimo:
```
pip install marimo matplotlib seaborn
```

## Usage
```
simulate-reads <parameters.info>
```
as a default, if no path was provided, it will use `./parameters.info`

where parameters.info file should be as follows.
```
# SYNTAX IS IMPORTANT
# LInes starting with # are comments
# name of the parameter: value
# : not = | where True/False first letter is uppercase.
random seed: 402

# GENOME SIMULATION PARAMETERS
reference file path: None
generate reference: True
GC percentage: 40
length of contigs: 1000000,10000,50000,200000 

# READS SIMULATION PARAMETERS
number of reads: 100000
read_length: 76
insert length: 100
insert length variations: 35
type of library: FFPE

# METHYLATION PARAMETERS
methylation library: False
percent methylation: 96

# PREFIX TO BE USED IN LOG AND OUTPUT FILES
prefix: ffpe_nometh
```
The above should be modified to your needs.

### Important considerations
Some systematic artifacts have a very low frequency and simulating few reads might not be enough to include even traces of it. In such case, use a higher number of reads (try one or more ordens of magnitude).
python-amcards 1.7.5
A wrapper for the AMcards API.

Getting Started | See the full docs at `Read the Docs <https://python-amcards.readthedocs.io/en/latest/>`_
==========================================================================================================
.. image:: https://i.ibb.co/tCrVfj6/readthedocs.png
    :target: https://python-amcards.readthedocs.io/en/latest/

Installation
------------
To install python-amcards, simply run this command in your terminal:

.. code-block::

    $ pip install python-amcards

Usage
-----
All interactions with the AMcards API are made through the `AMcardsClient <https://python-amcards.readthedocs.io/en/latest/amcards.html#amcards.amcards.AMcardsClient>`_ class.

First, create an `AMcardsClient <https://python-amcards.readthedocs.io/en/latest/amcards.html#amcards.amcards.AMcardsClient>`_ as follows:

.. code-block::

    >>> from amcards import AMcardsClient
    >>> client = AMcardsClient('youraccesstoken')

Here ``'youraccesstoken'`` will be replaced with a string containing your AMcards access token. You can generate one `here <https://amcards.com/user/generate-access-token/>`_.

Now we can perform all operations supported by the `client <https://python-amcards.readthedocs.io/en/latest/amcards.html#amcards.amcards.AMcardsClient>`_.

Let's try using ``send_card`` to send a card to a single recipient:

.. code-block::

        >>> res = client.send_card(
        ...     template_id='123',
        ...     initiator='myintegration123',
        ...     shipping_address={
        ...         'first_name': 'Ralph',
        ...         'last_name': 'Mullins',
        ...         'address_line_1': '2285 Reppert Road',
        ...         'city': 'Southfield',
        ...         'state': 'MI',
        ...         'postal_code': '48075',
        ...         'country': 'US'
        ...     }
        ... )
        >>> res.card_id
        1522873
        >>> res.total_cost
        442
        >>> res.message
        'Card created successfully!'
        >>> res.user_email
        'example@example.com'
        >>> res.shipping_address
        {'last_name': 'Mullins', 'address_line_1': '2285 Reppert Road', 'first_name': 'Ralph', 'country': 'US', 'state': 'MI', 'postal_code': '48075', 'city': 'Southfield'}

The `AMcardsClient <https://python-amcards.readthedocs.io/en/latest/amcards.html#amcards.amcards.AMcardsClient>`_ supports many more operations, for full documentation see `Read the Docs <https://python-amcards.readthedocs.io/en/latest/>`_.