HW_18

README.md

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+# Bioinformatics toolkit for beginner <a href=""><img src="https://cdn-icons-png.flaticon.com/512/8662/8662375.png" align="right" width="150" ></a>  <h3> Final homework of Python course at the BI</h3>
+
+The repository contains homework of the Python course during retraining program at the [Bioinformatics Institute(2023/2024)](https://bioinf.me/).
+
+The repository content is scripts, scripts designed to work with multiple biological data storage formats (such as FASTA and GBK), for processing biological sequences, parsing and for interacting with a telegram bot.
+
+## Table of content 
++ [Installation](https://github.com/LinaWhite15/Bioinformatics_toolkit_for_beginner/edit/Development/README.md#installation)
++ [Usage](https://github.com/LinaWhite15/Bioinformatics_toolkit_for_beginner/edit/Development/README.md#usage)
++ [Content](https://github.com/LinaWhite15/Bioinformatics_toolkit_for_beginner/edit/Development/README.md#content)
++ [Special gratitudes](https://github.com/LinaWhite15/Bioinformatics_toolkit_for_beginner/edit/Development/README.md#Special_gratitudes)
++ [Credits](https://github.com/LinaWhite15/Bioinformatics_toolkit_for_beginner/edit/Development/README.md#credits)
+
+## Installation
+To install the program, download files in main directory and, additionally, contents of the folder "data".
+OR
+You can simple clone this repository using
+```
+git clone [email protected]:LinaWhite15/Bioinformatics_toolkit_for_beginner.git
+```
+(for Linux and WSL users)
+**Python3 is required.**
+
+## Usage
+Before running the script, you must import required modules in your script. For example:
+```
+from bioinfUtils import genscan, GenscanOutput
+```
+or
+```
+import custom_random_forest
+```
+## Content
+
+### `bioinfUtils.py`  
+
+`genscan` - [GENSCAN](http://hollywood.mit.edu/GENSCAN.html) API     
+
+`telegram_logger` - decorator function for launching a Telegram bot, logging function execution     
+
+`DNASequence`, `RNASequence` and `AminoAcidSequence` -  classes for processing of biological sequences.     
+
+### `bio_files_processor.py`
+`OpenFasta`, `FastaRecord` - context manager and data class for handling with .fasta files. Provides less resource-intensive storage and iteration.
+
+`convert_multiline_fasta_to_oneline` - conwerts a multi-line FASTA to wide format
+
+`select_genes_from_gbk_to_fasta` - function for processing of GenBank files. The function selects genes flanking the given ones and saves its translated sequence into a FASTA file.
+
+### `custom_random_forest.py`
+`RandomForestClassifier` - custom implementation of random forest algorithm with parallelization
+
+### `test_bioinf_utils.py`
+Contains tests for functions from modules `bio_files_processor` and `bio_files_processor.py`.
+
+### `Showcases.ipynb`
+Hotebook with demonstration of `RandomForestClassifier`, `genscan`, `DNASequence`, and `AminoAcidSequence` functionality.
+
+## Special gratitudes
+Many thanks to the team of the Bioinformatics Institute, especially to the teachers and assistants of the Python program, for preparing and supporting such a wonderful course! It was a wonderful journey, or hopefully just the beginning of one.
+
+# Contacts
+If you have any comments or suggestions regarding this software, you can adress me using these contacts:      
+
+Belikova Angelina - [email protected]
+