semvec/pypi-packages huggingface dataset:
biomaj-process 3.0.19
BioMAJ process service

# About

[![PyPI version](https://badge.fury.io/py/biomaj-process.svg)](https://badge.fury.io/py/biomaj-process)

Microservice to manage the process execution of biomaj.

A protobuf interface is available in biomaj_process/message/message_pb2.py to exchange messages between BioMAJ and the download service.
Messages go through RabbitMQ (to be installed).

# Protobuf

To compile protobuf, in biomaj_process/message:

    protoc --python_out=. message.proto

# Development

    flake8  biomaj_process

    CONFIG=tests/config.yml python -m pytest -v tests/biomaj_tests.py

# Run

## Message consumer:

export BIOMAJ_CONFIG=path_to_config.yml
python bin/biomaj_process_consumer.py

## Web server

If package is installed via pip, you need a file named *gunicorn_conf.py* containing somehwhere on local server:

    def worker_exit(server, worker):
        from prometheus_client import multiprocess
        multiprocess.mark_process_dead(worker.pid)

If you cloned the repository and installed it via python setup.py install, just refer to the *gunicorn_conf.py* in the cloned repository.


    export BIOMAJ_CONFIG=path_to_config.yml
    rm -rf ..path_to/prometheus-multiproc
    mkdir -p ..path_to/prometheus-multiproc
    export prometheus_multiproc_dir=..path_to/prometheus-multiproc
    gunicorn -c ..path_to/gunicorn_conf.py biomaj_download.biomaj_process_web:app

Web processes should be behind a proxy/load balancer, API base url /api/process

A prometheus /metrics endpoint is exposed on web server


3.0.19
  Replace nose by pytest
3.0.18:
  Normalize yaml setup with other biomaj components
3.0.17:
  Fix yaml load warnings
3.0.16:
  In case of proxy comm failure, sleep a few seconds before retry
3.0.15:
  Add proc name in logs for waiting and result
3.0.14:
  Add env var BIOMAJ_HOST_DATA_DIR to use with *docker* process executor to specify data.dir location if different between host and container (if BIOMAJ_DATA_DIR not a subdirectory of BIOMAJ_DIR for example)
    If variable is not set, container wil mount data.dir between host and container,
    else will mount BIOMAJ_HOST_DATA_DIR:data.dir
3.0.13:
  Fix traefik prefix
3.0.12:
  Update pika dependency release
  Add tags for traefik support
3.0.11:
  Catch exception for microservices if remote server is not reachable
  Rename package for protobuf to avoid collisions
3.0.10:
  README doc fixes
  Add dependency banks additional volumes for Docker
3.0.9:
  Allow local_endpoint definition per service
  Fix volumes for docker with dependency banks
3.0.8:
  Fix #1, DRMAA needs colon in front of output and error path (mandatory depending on versions)
3.0.7:
  fix case if process desc or type is missing in bank properties
3.0.6:
  disable web thread logging
3.0.5:
  retry in case of contact failure with proxy
3.0.4:
  for docker, restrict directory to bank directory and dependencies
  add host in prometheus stats
3.0.3:
  fix prometheus + gunicorn multi process
  add consul supervision
3.0.2:
  add logging info
  execute docker processes in biomaj micro service
3.0.1:
  bug fixes
3.0.0:
  move process management out of biomaj main package
jwcnotipy 0.0.4
Provides a decorator that passes notifications to Slack
Requires Python: >=3.7

Welcome to jwcnotipy's documentation!
=====================================

This package was built to facillitate sending notifications to slack at runtime!

Notifications can be attached to specific functions with a handy decorator:

   ```
   from jwcnotipy import notify_on_exec

   @notify_on_exec(jwc_test_app, 'U037LP9TM8P')
   def sum(a,b):
      return a + b

   sum(3,1)
   ```

Or at any other key point using notify_me:

   ```
   from jwcnotipy import notify_me

   sum(3,1)
   notify_me(jwc_test_app, 'U037LP9TM8P')
   ```

The notifications are set up to post to a single channel defined by the
JWCNOTIPY_CHANNEL environment variable, but can be sent to another specific
channel by setting the channel keyword argument. NOTE only the user specified
in the function call can see the notifications! This will be extended to allow
a set of specific users and non-ephemeralised messages in a future build.


Contribute
----------

- Issue Tracker: github.com/$project/$project/issues
- Source Code: github.com/$project/$project

Support
-------

If you are having issues, please let us know.
We have a mailing list located at: project@google-groups.com

License
-------

The project is licensed under the BSD license.
clioetxt 2.3
A module to extract, transform (search, invert, format) and load text file or csv file
Keywords: txt file,csv file

This is the first python project that I created and shared with pypi.
I like working with excel file - importing and exporting data and data transformation using VBA, DAX and M-Code.
This module is created to handle text file data by importing data for searching, adding data, inverting data and formatting data.
Once the data is finalised, you can use "export_txt" function to convert it to text file.
I will work on adding more useful function later in future.

- Cheny Lioe -

Read the documentation after you install the package:
$ python -m pydoc -p 8000
Server ready at http://localhost:8000/
Server commands: [b]rowser, [q]uit
server> b
Then browse to clioetxt(package) to read documentation

Package contents:

1. load_txt
2. transform
3. merge
TEcount 0.5.0
Count read alignments on transposable elements subfamilies, families and classes.
Requires Python: >=3.7

# TEcount
A package to count reads mapping on transposable elements (TEs) subfamilies, families and classes.

## Features

TEcount counts high-throughput sequencing reads aligned on TEs on a reference genome.
It reports TE counts by subfamily, family and class on separate outputs.
In case of reads aligning on multiple TE loci, it counts only one alignment occurrence for each feature (i.e. subfamily, family or class).
It can use single or paired end BAM files, count in strand-specific manner and filter by a minimum read-TE overlap, among other features that can be discovered by running `TEcount --help`.

## Install
TEcount requires `python>=3.7`, `samtools>=1.14` and `bedtools>=2.30.0`. We strongly recommend installing TEcount, along with its requirements, in a conda environment:
```bash
# Create a conda environment with required packages
conda create -n tecount -c conda-forge -c bioconda "python>=3.7" "pip>=21.1" "samtools>=1.14" "bedtools>=2.30.0"

# Clone this repository (and optionally checkout to a specific version)
git clone https://github.com/bodegalab/tecount
cd tecount

# Install the package from the repository using pip from conda environment
conda activate tecount
pip install .
```

## Usage
Requires a BAM file sorted by coordinates and a bed6+3 file with subfamily, family and class in columns 7, 8 and 9.

```bash
TEcount -b <sorted_by_coord.bam> -r <rmsk.bed>
```

Example using test dataset:
```bash
TEcount -b ./test/Aligned.sortedByCoord.out.bam  -r ./test/rmsk.GRCm38.chr19.bed.gz
```

See all available parameters with:
```bash
TEcount --help
```

## Acknowledgements
Based on the transposable elements RNA-seq quantification strategy implemented in [1] by Sinha S.

## References
1. Marasca, F., Sinha, S., Vadalà, R. et al. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nat Genet 54, 180–193 (2022). https://doi.org/10.1038/s41588-021-00989-7
pythonloadingbar 0.0.1
Loading Bar for python
Keywords: python,loading,progress,progress bar,upload bar


# Python Loading Bar

### Usage:
```
loading(50, 10, 0.1, LOOP_SIZE, i+1,
        fg_text_color="green", bg_text_color="black", text_style="bold",
        fg_value_color="white", bg_value_color="black", value_style="normal",
        symbol_load='#', symbol_bg='.')
```