semvec/pypi-packages huggingface dataset:
biocli 1.0.1b1
Computational Biology tool for CLI use.
Requires Python: >=3.8

﻿
# CLI tool for Computational Biology

	Please read before use!

    Works with python version >= 3.9
    For Linux users only
    Works with `.txt` files only.
    Install requirements via pip3.
    Make the "compute" file executable using linux terminal typing `chmod +x compute` command

## How to use

Examples:
```console
$ ./compute biocli -h
usage: compute biocli [-h] {count,pattern,translate}
    
positional arguments:
  {count,pattern,translate}
    count                    Count feature to count the nucleotides and patterns in the 
                             given DNA or RNA sequence.
    pattern                  Pattern feature for finding given pattern in the given DNA 
                             or RNA sequence.
    translate                Translate feature to translate the given DNA sequence to 
                             RNA and vice versa.

optional arguments:
    -h, --help                 show this help message and exit
```
```console
$ ./compute biocli translate dna-to-rna "sample.txt" to_file=False
UGCUCCGCCGAACCAUUCAUGCGGGAUACGACUUGGAUGACAUAGGAAAUUCAUAAUUAUCGUGUCUAAGUAAUUGCAUGCAGGCUGCAA
UAACGUUGUUGGCCGAGCGUAAUACAAGAUUAGCCGCUGUUGAUGCUCAUUAGACGCGUUGGUAAAUUUGACGUUCUUAUGACCCCUACG
UAUAACAGAAUAGCCUCUGGUGACUUUUCUGAGCACCGAUCUCGCAAUAUAUUAGCCACUAUAUUAUCUAAGCCGAGCCAAUCAUUGAUA
CACAUAGUAAUGUCAGGACGUCGAACCUAGAUUGUAUGACUCCGCUAAGGUAUUCCGAGAGACACUAGGAUACUAGAUAUAUUCCCAAAG
UAAGGCGACGCCUAGUCUUUAGAGAGCGAGUAUGCCUUUGCCAAGUGUUGGAUGAGCCCGCCCCUUAAUAGGUGCUACGCUAGAGGCAAA
GCAUGUGGGCGGUGGCCACACUUCAAUCAGGUGGCGAGUAGACGCUUCAGCCCGUUCGAUCUUAAGUAUCAGUAUAGGGACUCGAGUACA
GUGUCCAAAUUACUGCGCUCGGUCCUAUGCUGACAAGGCGAACUCUGCAGAGAAUGGUCCGAAUUCACAUUCGGACAAUACGAUGUAGGA
CCGAACAAGCACAGUUUGAUUCGCCUCGGAAGACGGUGCAACUGAAACAGUAGAUCUCCUUAUCAAUGUAGGGCGAAGUACUGCCCGCGU
GAGGGCACCAGCAUCCAGUCUCGUUGCUGUUCGUAUGGGGAUCAACGGCGGGUUGUUCUUAAGAACAUCAGGAUGAGUUAAUCGAGAGUA
CUGAACCGCUAUUCGACACCGCAGGUUGCGACACCAAAUUGCCUAAACAUCAACAGCCUCAAUUACCUGCUGUCCACUCGAGCUUGGGGU
ACAGUGUUAUCCUUCACUUGAACGACAAGAUAAUGAACAUUGUGGACUUGCGUAUA
```


## Project layout
```console
├── biocli
   ├── biocli
   │   ├── count.py
   │   ├── pattern.py 
   │   ├── translate.py 
   │   ├── _errors.py
   │   ├── _helper.py
   │   ├── _sequence.py
   │   ├── __init__.py
   ├── compute 

```

### Contains:

	DNA to RNA sequence translator
	RNA to DNA sequence translator
	Pattern matcher
	Pattern counter
	Nucleotide counter
	Frequency counter

	Sample files added.

Built on top of DynaCLI by BST Labs. [Check it out!](https://github.com/BstLabs/py-dynacli)
cmsrucio-import 0.1.1
Utility tool to upload files and datasets from local machine to rucio
Requires Python: >=3.6,<4.0

# User DataManagement Tools


## Requirements

- initialise rucio (installs rucio_client) - `source /cvmfs/cms.cern.ch/rucio/setup-py3.sh`
- initalise proxy - `voms-proxy-init -voms cms -rfc -valid 192:00`
- export RUCIO_ACCOUNT=$USER 

## Additionally
pip3 install -r requirements.txt


## How to

Show list of available commands: `python3 upload.py --help`

Show help related to a specific commands (cmd): `python3 upload.py <cmd> --help`

<br>

To upload a local file and create a rule on it:
- Copy template from `lib/templates/file-upload.yml`
- Specify parameters:
    - `filePath`: location of local file 
    - `lfn`: lfn (logical file name) for the file - `store/user/rucio/<username>/<filename>`
    - `tempRSE`: temp RSE to use for the intermediate hop (can be left to template value)
    - `rse`: destination RSE/RSE Expression on which rule should be created
    - `lifetime`: life of rule
    - `copies`: number of copies required

- Execute: `python3 upload.py upload-file-yaml <yaml-file-path>`

<br>

To upload a dataset create a rule on it:
- Copy template from `lib/templates/dataset-upload.yml`
- Specify parameters:
    - `datasetPath`: location of folder to use as dataset 
    - `datasetName`: name of dataset conforming to CMS naming conventions
    - `tempRSE`: temp RSE to use for the intermediate hop (can be left to template value)
    - `rse`: destination RSE/RSE Expression on which rule should be created
    - `lifetime`: life of rule
    - `copies`: number of copies required

- Execute: `python3 upload.py upload-dataset-yaml <yaml-file-path>`


## Build Instructions

### Prerequisite

We will be using [poetry](https://python-poetry.org/) to build the package.

### Create a wheel package
```
cd CMSRucio/UserDMTools/cmsrucio_import

poetry build
```
### Installing from the wheel package
```
pip3 install --user dist/cmsrucio_import-0.1.0-py3-none-any.whl
```