Metadata-Version: 2.1
Name: biofile-kit
Version: 0.0.1
Summary: Bioinformatics File Operations Toolkit.
Author: Wenlin Xu
Author-email: wenlinxu.njfu@outlook.com
Requires-Python: >=3.8,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: pybioinformatic (==1.2.3)
Description-Content-Type: text/markdown

# Introduction
**BioFileKit: Designed to provide bioinformatics researchers and developers with a powerful, user-friendly and 
extensible Python toolkit, it focuses on simplifying the reading, writing, conversion, parsing and basic operations of 
various biological data file formats. Say goodbye to reinventing the wheel and the cumbersome format analysis, and 
focus on your scientific discoveries!**

# Install
```
pip install biofile-kit
```

# Usage example
## Generate random nucleotide sequences
```shell
fasta_tools random_nucl -n seq1,seq2 -l 1000,1200
```
```
>seq1 length=1000
CGCCAGGCCTGCCCTGCGACGGAGGTTCCCCGTATGACTGCCCTATATCATTCCTGCTAAACTCAATCCACAAGATCAATTCACTCCGGGGAACAACTGCCACTAGAAACCGTAGGTTACCATCAATAGTTCCCCACTTGGAGGAAGAAGTCTTTGAAGCAGGTTGTCATCCAGCATTCTTTCTAAACGTCATTGGACATAGGGGTAAGCTCATATCCTCTCCCAACCATTCAGAAGTCCATGACCATGTCCGGTGCAAATTTGAAAGTCATGATGGTGAGGGAGCAAGAGAGCGCAGATCACGGATAAGTATTAAAAAGTGCTGTCGAGGCCGCAGTGGAAGTGACTAATTGGCTGATGCACGGACCTCCAGTGTACAGCTCATGTTTCAGGTGCGTCGGACTGTCAGTGACTCAATTTTCTGGGCCCAACTCCGCGTTCGGTGGATTAGTAACTATAGTGGTTGCATGAGGTACTGAGATTGAGCCGTGAAAAGCATTCAAAGTGCGGTTCCTCAACCTATTATTATTAAGACATAAGTTTGCTAGCGCTTTGTTGCAATCGTGTCGTGGAATGCGATTGATGCTTAGCAGTTTCCGGGAAGTACGGACTCATGCCGTTATGTGCGCCAACAAACAGCGCGTGTTTCATTTCGCGCCGGTCGCCTGGCGCGTGTTATGGGATCGCACTTCACCGTGCTGATATCGCTGAGGCGAGGGTTCCTCGAGATATTGGCTTGGCTCGCCAGGCAGTAGTCGTGGTCAGCCCGACTTGGCACGCTAAAGACGAGCCCACGTGCATTCGGTCGGAATCAGTTAGACGTCGAACGATTCGATCCAGCGTGAGGCCTATCCTTTGCCCATTTAACTCCGTATTCACGGTCTCCTTGATACATAGTGTACTTAGTGTTACCAGCGAACTCCGACGCGGACAGTGTCCTCGGAGTATTACCTCCAAAGAAATTCTCGGGCCGAACAGCGTAGTCTATACCGCCTGGGTG
>seq2 length=1200
ATAGGTGTAGTGTGTCTTCATCTTGATGTAAGTTCGTTCACCCAGATCTGCTAAAACGCATGGCATTTTTTTCGCATACGGTCCACTGGCACTATATGATTCCCAGTACTTCGCAGATTTGGGGGGGTAAGAGTCCGCGGAAGCGTTGTTCTGACGCGTACGCATGTTCGGTATTTTTTACGGGTGAGTTGCATCGGTTGTGTATTGGTCCATGTTAAGACGGTTATCGGGCAGGCTTCTCAATGCGGTGAGTCGGGAAGACACTAGCCAGCGAAATTATGTGATCGCTGGAATAGGATCGATGTAGCAACGACACTTTCCTGGCCTACAGACGGACTTGGACCGGATCAATCGTCTTATATAATAATACACGTCGCAGAACGGTCTGTGTATAGGACCGGTAGAATGAGTAGTTCATACTCCGGCCCGCAGGTACCCCTGTACGCATGAAAGTCCAAGCTCTCGCTGAACCGACACCTCTAGCCGAGGTACGTATGCATGACCTGGTTGTTCTCTTCGGGTCACGACAGTTGCCTATTTACGCTCGGATACCAGGAAACTTTGCCGGGAGTTCGCCCCCAGTAGTTCCCGGGTTGGGGTCGGGGTGTTCTGCCGATTACCGGATGTATCTCACCTGAGATTCAGCATCGGTGCGAACATCGTGAATCCTAAAGGTTGAACAAAGGAAGGCCTCCATGCGTTGGAAAGTCCTCGAAGTGGAGAAGTCTATCGTAGATCAACCGATAGGCAATGAAAAGAAAAAGCGCAACAGACGCCACGCTTCTAGATCGCAGTTGGCCTTTTAATGGCGAATCCATTTACCGAGCGAAGAAAAAGCCTGGCTAGCTTGTTTAAAACTGGTAACACTGAATCTCCGAAAGAGTAGCTATAGGCTCCCAGCACAGCCTGCGGCTGGCGCCAACGCCTAACGAAAATGCCAATCCACTTAGTTGTGTTAACTGTCTCCCCACTATATGCGGCTTACCAGGGAGTGTAATTTCTGGCGATGACCAGCGTTTCCTTTGGGTTCCGTCGAATTCCTTAGATCTAGGACAGCAGTTCGAATTACTTGGCGTGGTCGCATCAGGACTTCGCGTAGTGGCTATCCAGATCATAGACTGAGTCACGTATTTGACGCCAGACCTAAGACCCCACGATGGTTTCTAGTCGTAACTTGAGTGAGCTAGCTCGCCTCGTGTC
```
## ORF prediction
```shell
fasta_tools random_nucl -n seq1,seq2 -l 1000,1200 | fasta_tools ORF_finder -c -
```
```
>seq1 length=42 ORF_prediction
MRLMLSSFREVRTHAVMCANKQRVFHFAPVAWRVLWDRTSPC*
>seq2 length=87 ORF_prediction
MIWIATTRSPDATTPSNSNCCPRSKEFDGTQRKRWSSPEITLPGKPHIVGRQLTQLSGLAFSLGVGASRRLCWEPIATLSEIQCYQF*
```

