Metadata-Version: 2.1
Name: biofile-kit
Version: 0.0.2
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 (>=1.2.4,<2.0.0)
Description-Content-Type: text/markdown

# Introduction
**BioFileKit: A Python command-line toolkit dedicated to simplifying the reading, writing, conversion, 
parsing and basic operations of various biological data file formats.**

# 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*
```

